No MPI compilation.

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=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
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
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=

Undefined keyword(s):
allEnergiesFileOutputFreq     <int,positive>
BSDLFile                      <string,non-empty>
BSDLFileOutputFreq            <int,positive>
DCDFileMinimalImage           <boolean>
DCDFileOutputFreq             <int,positive>
DCDVELFile                    <string,non-empty>
DCDVELFileMinimalImage        <boolean>
DCDVELFileOutputFreq          <int,positive>
diffusionFile                 <string,non-empty>
diffusionFileOutputFreq       <int,positive>
dihedralMultPSF               <boolean>
dihedralsFile                 <string,non-empty>
dihedralsFileMinimalImage     <boolean>
dihedralsFileOutputFreq       <int,positive>
dihedralsIndex                <int,non-negative>
dihedralsSetfile              <string,non-empty>
doallEnergiesFile             <boolean>
doBSDLFile                    <boolean>
doDCDFile                     <boolean>
doDCDVELFile                  <boolean>
dodiffusionFile               <boolean>
dodihedralsFile               <boolean>
dofinPDBPosFile               <boolean>
dofinXYZBinPosFile            <boolean>
dofinXYZBinVelFile            <boolean>
dofinXYZPosFile               <boolean>
dofinXYZVelFile               <boolean>
domomentumFile                <boolean>
dopaulFile                    <boolean>
doPaulLowFile                 <boolean>
doPDBPosFile                  <boolean>
doREMExchangeRatesFile        <boolean>
doREMHistoryFile              <boolean>
dostateFile                   <boolean>
doTempFile                    <boolean>
doXYZBinPosFile               <boolean>
doXYZBinVelFile               <boolean>
doXYZForceFile                <boolean>
doXYZPosFile                  <boolean>
doXYZVelFile                  <boolean>
eigfile                       <string,non-empty>
eigvalfile                    <string,non-empty>
finPDBPosFileMinimalImage     <boolean>
finXYZBinPosFile              <string,non-empty>
finXYZBinPosFileMinimalImage  <boolean>
finXYZBinVelFile              <string,non-empty>
finXYZPosFileMinimalImage     <boolean>
momentumFile                  <string,non-empty>
momentumFileOutputFreq        <int,positive>
paulFile                      <string,non-empty>
paulFileOutputFreq            <int,positive>
paulOmega                     <real,non-negative>
paulOmegaZ                    <real,non-negative>
PDBPosFile                    <string,non-empty>
PDBPosFileMinimalImage        <boolean>
REMExchangeRatesFile          <string,non-empty>
REMExchangeRatesFileOutputFreq<int,positive>
REMHistoryFile                <string,non-empty>
REMHistoryFileOutputFreq      <int,positive>
ScreenOutputFreq              <int,positive>
ScreenPaulTrap                <boolean>
stateFile                     <string,non-empty>
stateFileOutputFreq           <int,positive>
statesInputFile               <string,non-empty>
TemperatureSeparateWater      <boolean>
TempFile                      <string,non-empty>
TempFileOutputFreq            <int,positive>
velfile                       <string,non-empty>
XYZBinPosFile                 <string,non-empty>
XYZBinPosFileMinimalImage     <boolean>
XYZBinPosFileOutputFreq       <int,positive>
XYZBinVelFile                 <string,non-empty>
XYZBinVelFileOutputFreq       <int,positive>
XYZForceFileOutputFreq        <int,positive>
XYZPosFile                    <string,non-empty>
XYZPosFileMinimalImage        <boolean>
XYZPosFileOutputFreq          <int,positive>
XYZVelFile                    <string,non-empty>
XYZVelFileOutputFreq          <int,positive>
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Using seed 1234.
Using report level 0.
Recoverable Error:  [PDB::read] Record unknow:'CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1'.
Using PDB posfile 'alanC7axial_wb5_min_eq.pdb' (283).
Using temperature 310K for the velocities  (283).
Using PSF file 'alan_wb5.psf' (283).
Using PAR file 'par_all27_prot_lipid.inp', new charmm force field.
Hint:  Reduced fast delta max of ExclusionTable from 31 to 10.
Random temperature : 323.034K
Removed linear momentum: (0.250711,-0.0617995,-0.214577)
Removed angular momentum : (-2.6321,4.89027,1.79862)
Actual start temperature : 321.989K
Using MD integrator. 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Virial tensor : false
Molecular virial tensor : false
Hint:  PME: alpha=0.312341327434087, V=3251.67, Rc=10, Kc =2.32189682086915, n=7, accuracy=1e-06, interpolation=BSpline, order=4.
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Output allEnergiesFile alanine.out.energy 100 1 0 1 false false.
Output DCDFile alanine.out.dcd 100 true.
Output finPDBPosFile alanine.EW.fin.pdb true.
Output finXYZPosFile alanine.EW.fin.pos.xyz true.
Output finXYZVelFile alanine.EW.fin.vel.xyz.
Output Screen true 100.
Output XYZForceFile alanine.EW.force.xyz 100.
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
integrator {
  Level 0 LangevinImpulse {
      timestep 1
      temperature 310
      gamma 1
      seed 1234
      numsteps 0
    Force Improper
    Force Dihedral
    Force Bond
    Force Angle
    Force LennardJones CoulombEwaldReal -switchingFunction Cn -switchingFunction Cutoff -algorithm NonbondedCutoff
      -switchon 8	 # Cn swf switch on
      -switchoff 8	 # Cn swf switchoff
      -cutoff 8	 # Cn swf cutoff
      -n 2	 # Cn swf smothness
      -alpha 0.275106390571206	 # Ewald splitting
      -cutoff 10	 # cutoff swf cutoff
      -cutoff 10	 # algorithm cutoff
    Force Coulomb -algorithm PMEwald -reciprocal -correction -interpolation BSpline
      -gridsize 16 18 16
      -cutoff 10	 # Rc cutoff
      -order 4	 # interpolation
      -accuracy 1e-06
      -alpha 0.312341327434087	 # splitting
  }
}
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Atoms                : 283
AtomTypes            : 10
Bonds                : 195
Angles               : 123
Dihedrals            : 42 (45)
Impropers            : 4
Molecules            : 88
Water                : 87
Pairs                : 203
Degree of freedom    : 846
Molecule pair dist's : true
Exclusion pairs      : 359
Max exclusion dist   : 10
Time                 : 0
CellManager          : Cubic
BoundaryConditions   : Periodic orthogonal
coulombScalingFactor : 1
exclude              : scaled1-4
cellBasisVector1     : 14.58 0 0
cellBasisVector2     : 0 15.52 0
cellBasisVector3     : 0 0 14.37
cellorigin           : 0 0 0
cellSize             : 5
Atom density         : 0.0870322931312387
Atom/cell            : 23.5833333333333
Real cell size       : (7.29,5.17333333333333,7.185)
Cell dimension       : (2,3,2)
Simulation box       : (7.47,-73.94,-40.635)-(22.05,-58.42,-26.265) (14.58,15.52,14.37)
Particle             : (7.497,-73.934,-40.632)-(22.031,-58.478,-26.293) (14.534,15.456,14.339)
Particle extended    : (5.553,-74.421,-40.882)-(22.708,-57.751,-25.66) (17.155,16.67,15.222)
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Step :          0, Time :              0.000 [ps], TE :        -580.0240 [kcal/mol], T :   321.9891 [K], V :          3251.67 [AA^3]
Step :        100, Time :              0.100 [ps], TE :        -579.5632 [kcal/mol], T :   319.6946 [K], V :          3251.67 [AA^3]
Timing : wall: 1.57020[s] real, 1.46478[s] user, 0.09698[s] sys, run: 1.35360[s], integration: 1.30520[s], forces: 1.26509[s].