No MPI compilation. ###### # # # # ##### #### ##### #### ## ## #### # # # # # # # # # # # # # # # # # ###### # # # # # # # # # # # # # # ##### # # # # # # # # # # # # # # # # # # # # # # # # # # #### # #### # # #### ###### =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Please cite T. Matthey, T. Cickovski, S. S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach, and J. A. Izaguirre. ProtoMol: An object-oriented framework for prototyping novel algorithms for molecular dynamics. ACM Trans. Math. Softw., 30(3):237­265, 2004. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= ProtoMol Version 2.0.4 jesus Mar 19 2007 12:18:54 Linux localhost.localdomain 2.6.9-42.0.8.ELsmp #1 SMP Tue Jan 23 13:01:26 EST 2007 i686 i686 i386 GNU/Linux icpc -Wall -wd810,383,981,279,444,1572 -O3 -ip -DNDEBUG 32-bit Intel(R) C++ Compiler for 32-bit applications, Version 8.1 Build 20060606Z Package ID: l_cc_pc_8.1.038 Copyright (C) 1985-2006 Intel Corporation. All rights reserved. Version 8.1 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Information: protomol@cse.nd.edu http://protomol.sourceforge.net =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Forces with 'VacuumCubic' topology: =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Angle Bond Coulomb -algorithm FullEwald -correction -alpha # splitting -accuracy -j -algorithm FullEwald -real -alpha # splitting -accuracy -j -algorithm FullEwald -real -correction -alpha # splitting -accuracy -j -algorithm FullEwald -real -reciprocal -correction -alpha # splitting -accuracy -j -algorithm FullEwald -reciprocal -alpha # splitting -accuracy -j -algorithm FullEwald -reciprocal -correction -alpha # splitting -accuracy -j -algorithm MultiGrid -interpolation Hermite -kernel C1 -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C1 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C1 -smooth -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C1 -smooth -correction -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C2 -smooth -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -smooth -correction -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C3 -smooth -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -smooth -correction -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C4 -smooth -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -smooth -correction -s # smoothing distance -h -origin -levels -order # interpolation -ratio -algorithm NonbondedSimpleFull -blocksize -algorithm PMEwald -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -algorithm PMEwald -real -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -algorithm PMEwald -real -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -algorithm PMEwald -reciprocal -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -algorithm PMEwald -reciprocal -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -j -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementC2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction ComplementCn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementCutoff -algorithm NonbondedSimpleFull -cutoff # cutoff swf cutoff -blocksize -switchingFunction ComplementShift -algorithm NonbondedSimpleFull -cutoff # shift swf cutoff -blocksize -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff CoulombDiElec -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementC2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction ComplementCn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementCutoff -algorithm NonbondedSimpleFull -cutoff # cutoff swf cutoff -blocksize -switchingFunction ComplementShift -algorithm NonbondedSimpleFull -cutoff # shift swf cutoff -blocksize -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff CoulombTable -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff Dihedral ElectricField -switchingFunction C1 -cutoff # C1 swf cutoff -origin -e # Electric field source, [e] -a # Scaling factor ExternalGravitation -g # external parallel gravitation [m/s^2] ExternalMagneticField -B # External magnetic field [T] Friction -k -rnd Gravitation -algorithm NonbondedSimpleFull -G -blocksize Haptic -port -trate -timeout -step_inc -wait HarmDihedral -kbias # potential bias constant -dihedral -angle # reference angle -180 to 180 -others Improper LennardJones -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementC2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction ComplementCn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementCutoff -algorithm NonbondedSimpleFull -cutoff # cutoff swf cutoff -blocksize -switchingFunction ComplementShift -algorithm NonbondedSimpleFull -cutoff # shift swf cutoff -blocksize -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff LennardJones Coulomb -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction C1 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -blocksize -switchingFunction Cn -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -blocksize -switchingFunction ComplementC2 -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementCn -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplimentCnCn -switchingFunction C1 -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff LennardJones CoulombDiElec -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction C1 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -blocksize -switchingFunction Cn -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -blocksize -switchingFunction ComplementC2 -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementCn -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplimentCnCn -switchingFunction C1 -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff LennardJones CoulombEwaldReal -switchingFunction C1 -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJones CoulombEwaldRealTable -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff LennardJones CoulombMultiGridDirect -kernel C1 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJones CoulombMultiGridDirectTable -kernel C1 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJonesTable -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff LennardJonesTable CoulombTable -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff MagneticDipole -algorithm NonbondedSimpleFull -chi -r -omega -phi -H -d -blocksize -switchingFunction C1 -algorithm NonbondedCutoff -chi -r -omega -phi -H -d -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -chi -r -omega -phi -H -d -cutoff # C1 swf cutoff -blocksize MagneticDipoleMirror -chi -r -H -d MollyAngle MollyBond MollyCoulomb -r0 # range swf from -r1 # range swf to -cutoff # C1 swf cutoff MollyLennardJones -r0 # range swf from -r1 # range swf to -switchon # C2 swf switch on -cutoff # C2 swf cutoff MollyLennardJonesCoulomb -r0 # range swf from -r1 # range swf to -switchon # C2 swf switch on -cutoff # C2 swf cutoff PaulTrap -omegaR -omegaZ -alpha -r0 -u0 -k Spherical -center -radius -k # external force constant -j # exponent for the potential function SphericalRestraint -k # external force constant Alias: CoulombEwald : Coulomb -algorithm FullEwald -real -reciprocal -correction (Coulomb -algorithm FullEwald -real -reciprocal -correction) CoulombPME : Coulomb -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline (Coulomb -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline) =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Forces with 'PeriodicCubic' topology: =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Angle Bond Coulomb -algorithm FullEwald -correction -alpha # splitting -accuracy -algorithm FullEwald -real -alpha # splitting -accuracy -algorithm FullEwald -real -correction -alpha # splitting -accuracy -algorithm FullEwald -real -reciprocal -correction -alpha # splitting -accuracy -algorithm FullEwald -reciprocal -alpha # splitting -accuracy -algorithm FullEwald -reciprocal -correction -alpha # splitting -accuracy -algorithm MultiGrid -interpolation Hermite -kernel C1 -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C1 -smooth -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C1 -smooth -correction -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C2 -smooth -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C2 -smooth -correction -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C3 -smooth -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C3 -smooth -correction -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -correction -s # smoothing distance -algorithm MultiGrid -interpolation Hermite -kernel C4 -smooth -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm MultiGrid -interpolation Hermite -kernel C4 -smooth -correction -s # smoothing distance -toplevelgrid -levels -order # interpolation -ratio -algorithm NonbondedSimpleFull -blocksize -algorithm PMEwald -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -algorithm PMEwald -real -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -algorithm PMEwald -real -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -algorithm PMEwald -reciprocal -correction -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -algorithm PMEwald -reciprocal -interpolation BSpline -gridsize -cutoff # Rc cutoff -order # interpolation -accuracy -alpha # splitting -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C1 -algorithm NonbondedFull -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction C1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -blocksize -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementC2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction ComplementCn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementCutoff -algorithm NonbondedSimpleFull -cutoff # cutoff swf cutoff -blocksize -switchingFunction ComplementShift -algorithm NonbondedSimpleFull -cutoff # shift swf cutoff -blocksize -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedFull -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -blocksize -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedFull -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedFull -cutoff # shift swf cutoff -cutoff # algorithm cutoff -blocksize CoulombDiElec -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff CoulombEwaldReal -switchingFunction Cutoff -algorithm NonbondedCutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff CoulombEwaldRealTable -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff CoulombTable -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff Dihedral ElectricField -switchingFunction C1 -cutoff # C1 swf cutoff -origin -e # Electric field source, [e] -a # Scaling factor ExternalGravitation -g # external parallel gravitation [m/s^2] ExternalMagneticField -B # External magnetic field [T] Friction -k -rnd Gravitation -algorithm NonbondedSimpleFull -G -blocksize Haptic -port -trate -timeout -step_inc -wait HarmDihedral -kbias # potential bias constant -dihedral -angle # reference angle -180 to 180 -others Improper LennardJones -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C1 -algorithm NonbondedFull -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction C2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -blocksize -switchingFunction Cn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementC2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction ComplementCn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction ComplementCutoff -algorithm NonbondedSimpleFull -cutoff # cutoff swf cutoff -blocksize -switchingFunction ComplementShift -algorithm NonbondedSimpleFull -cutoff # shift swf cutoff -blocksize -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedFull -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -blocksize -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedFull -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Shift -algorithm NonbondedFull -cutoff # shift swf cutoff -cutoff # algorithm cutoff -blocksize LennardJones Coulomb -algorithm NonbondedSimpleFull -blocksize -switchingFunction C1 -switchingFunction Shift -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction C1 -switchingFunction Shift -algorithm NonbondedFull -cutoff # C1 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -blocksize -switchingFunction C2 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -blocksize -switchingFunction C2 -switchingFunction C1 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -blocksize -switchingFunction Cn -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplementC2 -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplementCn -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # C1 swf cutoff -blocksize -switchingFunction ComplimentCnCn -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cutoff -switchingFunction Cutoff -algorithm NonbondedFull -cutoff # cutoff swf cutoff -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -blocksize LennardJones CoulombEwaldReal -switchingFunction C1 -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -switchingFunction Cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -alpha # Ewald splitting -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJones CoulombEwaldRealTable -switchingFunction C1 -algorithm NonbondedCutoff -cutoff # C1 swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction Cutoff -algorithm NonbondedCutoff -cutoff # cutoff swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff LennardJones CoulombMultiGridDirect -kernel C1 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJones CoulombMultiGridDirectTable -kernel C1 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C1 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C2 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C3 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction C2 -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff -kernel C4 -switchingFunction ComplimentCnCn -switchingFunction Cutoff -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff for table look up -s # MG smoothing distance -cutoff # cutoff swf cutoff -cutoff # algorithm cutoff LennardJonesTable -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # algorithm cutoff LennardJonesTable CoulombEwaldRealTable -switchingFunction C2 -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction Cn -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # cutoff swf cutoff -alpha # splitting -cutoff # algorithm cutoff LennardJonesTable CoulombTable -switchingFunction C2 -switchingFunction Shift -algorithm NonbondedCutoff -switchon # C2 swf switch on -cutoff # C2 swf cutoff -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction Cn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # Cn swf switch on -switchoff # Cn swf switchoff -cutoff # Cn swf cutoff -n # Cn swf smothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff -switchingFunction ComplimentCnCn -switchingFunction Shift -algorithm NonbondedCutoff -switchon # CmpCnCn swf switch on -switchoff # CmpCnCn swf switchoff -cutoff # CmpCnCn swf cutoff -n # CmpCnCn swf smoothness -cutoff # shift swf cutoff -cutoff # algorithm cutoff MagneticDipole -algorithm NonbondedSimpleFull -chi -r -omega -phi -H -d -blocksize -switchingFunction ComplementC1 -algorithm NonbondedSimpleFull -chi -r -omega -phi -H -d -cutoff # C1 swf cutoff -blocksize MagneticDipoleMirror -chi -r -H -d MollyAngle MollyBond MollyCoulomb -r0 # range swf from -r1 # range swf to -cutoff # C1 swf cutoff MollyLennardJones -r0 # range swf from -r1 # range swf to -switchon # C2 swf switch on -cutoff # C2 swf cutoff MollyLennardJonesCoulomb -r0 # range swf from -r1 # range swf to -switchon # C2 swf switch on -cutoff # C2 swf cutoff Alias: CoulombEwald : Coulomb -algorithm FullEwald -real -reciprocal -correction (Coulomb -algorithm FullEwald -real -reciprocal -correction) CoulombPME : Coulomb -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline (Coulomb -algorithm PMEwald -real -reciprocal -correction -interpolation BSpline) =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=