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 27 2007 04:24:35
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 -inline_debug_info -restrict
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>
cellBasisVector1              <coordinates,non-zero>
cellBasisVector2              <coordinates,non-zero>
cellBasisVector3              <coordinates,non-zero>
cellorigin                    <coordinates>
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 1.
Using PDB posfile 'alanC7axial_wb5_min_eq.pdb' (22).
Using temperature 310K for the velocities  (22).
Recoverable Error:  [PSF::read] Record !NUMLP with 0 entries not recognized.
Using PSF file 'blockdialanineHassan05.psf' (22).
Using PAR file 'par_all27_prot_lipid.inp', new charmm force field.
Coulomb SCPISM Parameter Table!!!
C	0.5298	0.5	0.5	0.7273	0.77	0.0052	0	31	6.6	0.8	2	
CA	0.5192	0.5	0.5	0.7206	0.77	0.0052	0	31	6.6	0.8	1.9924	
CAL	0	0	0	0	0	0	0	0	0	0	1.367	
CC	0.497	0.5	0.5	0.705	0.77	0.0052	0	31	6.6	0.8	2	
CD	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	2	
CE1	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	2.09	
CE2	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	2.08	
CM	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	2.1	
CP1	0.4763	0.5	0.5	0.6901	0.77	0.0052	0	31	6.6	0.8	2.275	
CP2	0.4599	0.5	0.5	0.6782	0.77	0.0052	0	31	6.6	0.8	2.175	
CP3	0.4627	0.5	0.5	0.6802	0.77	0.0052	0	31	6.6	0.8	2.175	
CPA	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	1.8	
CPB	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	1.8	
CPH1	0.4538	0.5	0.5	0.6736	0.77	0.0052	0	31	6.6	0.8	1.8	
CPH2	0.4974	0.5	0.5	0.7053	0.77	0.0052	0	31	6.6	0.8	1.8	
CPM	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	1.8	
CPT	0.5217	0.5	0.5	0.7229	0.77	0.0052	0	31	6.6	0.8	1.8	
CS	0	0	0	0	0.77	0.0052	0	31	6.6	0.8	2.2	
CT1	0.5209	0.5	0.5	0.7217	0.77	0.0052	0	31	6.6	0.8	2.275	
CT2	0.5298	0.5	0.5	0.7273	0.77	0.0052	0	31	6.6	0.8	2.175	
CT3	0.5082	0.5	0.5	0.7129	0.77	0.0052	0	31	6.6	0.8	2.06	
CY	0.524	0.5	0.5	0.7239	0.77	0.0052	0	31	6.6	0.8	1.9924	
DUM	0	0	0	0	0	0	0	0	0	0	0	
FE	0	0	0	0	0	0	0	0	0	0	0.65	
H	0.4906	0.6259	0.5	0.7004	0.37	0.0052	1	1.2	3.68	1.82	0.2245	
HA	0.53	0.5	0.5	0.728	0.37	0.0052	0	17	9.6	1.1	1.32	
HA1	0	0	0	0	0.37	0.0052	0	17	9.6	1.1	0.2245	
HA2	0	0	0	0	0.37	0.0052	0	17	9.6	1.1	0.2245	
HB	0.4858	0.5	0.5	0.697	0.37	0.0052	0	17	9.6	1.1	1.32	
HC	0.53	8.6746	0.5	0.728	0.37	0.0052	1	1.2	3.68	1.82	0.2245	
HE	0	0	0	0	0	0	0	0	0	0	1.48	
HP	0.5274	0.5	0.5	0.7262	0.37	0.0052	0	17	9.6	1.1	1.3582	
HR1	0.4651	0.5	0.5	0.682	0.37	0.0052	0	17	9.6	1.1	0.9	
HR2	0.458	0.5	0.5	0.6768	0.37	0.0052	0	17	9.6	1.1	0.7	
HR3	0.4893	0.5	0.5	0.6995	0.37	0.0052	0	17	9.6	1.1	1.468	
HS	0.4859	0.5	0.5	0.6971	0.37	0.0052	0	17	9.6	1.1	0.45	
HT	0.4906	2.38	0.5	0.7004	0.37	0.0052	1	1.2	3.68	1.82	0.2245	
N	0.4894	0.5	0.5	0.6996	0.74	0.0052	0	60	6.9	0.62	1.85	
NC2	0.5299	0.5	0.5	0.7279	0.74	0.0052	0	60	6.9	0.62	1.85	
NE	0	0	0	0	0	0	0	0	0	0	1.53	
NH1	0.5103	0.5	0.5	0.7144	0.74	0.0052	0	60	6.9	0.62	1.85	
NH2	0.5045	0.5	0.5	0.7103	0.74	0.0052	0	60	6.9	0.62	1.85	
NH3	0.53	0.5	0.5	0.728	0.74	0.0052	0	60	6.9	0.62	1.85	
NP	0.4894	0.5	0.5	0.6996	0.74	0.0052	0	60	6.9	0.62	1.85	
NPH	0	0	0	0	0.74	0.0052	0	60	6.9	0.62	1.85	
NR1	0.4598	0.5	0.5	0.6781	0.74	0.0052	0	60	6.9	0.62	1.85	
NR2	0.4839	19.4824	0.6956	0.5	0.74	0.0052	2	60	6.9	0.62	1.85	
NR3	0.4742	0.5	0.5	0.6886	0.74	0.0052	0	60	6.9	0.62	1.85	
NY	0.5284	0.5	0.5	0.7269	0.74	0.0052	0	60	6.9	0.62	1.85	
O	0.481	4.0085	0.5	0.6935	0.74	0.0052	2	40	7.1	0.74	1.7	
OB	0	0	0	0	0.74	0.0052	0	40	7.1	0.74	1.7	
OC	0.6	8.1838	0.5	0.7746	0.74	0.0052	2	40	7.1	0.74	1.7	
OH1	0.4843	3.3433	0.5	0.6959	0.74	0.0052	2	40	7.1	0.74	1.77	
OM	0	0	0	0	0.74	0.0052	0	40	7.1	0.74	1.7	
OS	0	0	0	0	0.74	0.0052	0	40	7.1	0.74	1.77	
OT	0	0	0	0	0	0	0	40	7.1	0.74	1.7682	
S	0.5054	5.0037	0.5	0.7109	1.04	0.0052	2	60	6.5	0.62	2	
SM	0.5054	0.5	0.5	0.7109	1.04	0.0052	0	60	6.5	0.62	1.975	
SS	0	0	0	0	1.04	0.0052	0	60	6.5	0.62	2.2	
ZN	0	0	0	0	0	0	0	0	0	0	1.09	
Hint:  Reduced fast delta max of ExclusionTable from 31 to 10.
Random temperature : 415.626K
Removed linear momentum: (-0.217826,-0.129107,0.327183)
Removed angular momentum : (0.436469,-0.558937,-0.386322)
Actual start temperature : 462.495K
Using MD integrator. 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Initial SASA Values:
Solvent fraction 
CT3
0.206063
HA
0.182853
HA
0.182853
HA
0.182853
C
0.2134
O
0.331228
NH1
0.452038
H
0.0361853
CT1
0.182657
HB
0.182853
CT3
0.206063
HA
0.182853
HA
0.182853
HA
0.182853
C
0.2134
O
0.331228
NH1
0.452038
H
0.0361853
CT3
0.206063
HA
0.182853
HA
0.182853
HA
0.182853
Virial tensor : false
Molecular virial tensor : false
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Output allEnergiesFile alanine.out.energy 10 1 0 1 false false.
Output DCDFile alanine.out.dcd 10 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 10.
Output XYZForceFile alanine.EW.forceBorn.xyz 10.
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
integrator {
  Level 0 LangevinImpulse {
      timestep 1
      temperature 310
      gamma 91
      seed 1234
    Force CoulombBornRadii -switchingFunction Cutoff -algorithm NonbondedCutoff
      -cutoff 6	 # cutoff swf cutoff
      -cutoff 6	 # algorithm cutoff
  }
}
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Atoms                : 22
AtomTypes            : 8
Bonds                : 21
Angles               : 36
Dihedrals            : 42 (45)
Impropers            : 4
Molecules            : 1
Water                : 0
Pairs                : 29
Degree of freedom    : 63
Molecule pair dist's : true
Exclusion pairs      : 98
Max exclusion dist   : 10
Time                 : 0
CellManager          : Cubic
BoundaryConditions   : Vacuum orthogonal
coulombScalingFactor : 1
exclude              : scaled1-4
cellSize             : 5
Atom density         : 0.108900866111517
Atom/cell            : 13.6126082639397
Real cell size       : (5,5,5)
Cell dimension       : (2,2,1)
Simulation box       : (-inf,-inf,-inf)-(inf,inf,inf) (inf,inf,inf)
Particle             : (5.553,-72.653,-35.234)-(11.672,-65.802,-30.415) (6.119,6.851,4.819)
Particle extended    : (5.553,-72.653,-35.234)-(11.672,-65.802,-30.415) (6.119,6.851,4.819)
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Step :          0, Time :              0.000 [fs], TE :          28.9506 [kcal/mol], T :   462.4952 [K], V :           202.02 [AA^3]
SASA Values:
Solv. frac. 	Born radii
CT3
0.21 		1.5
HA
0.18 		1.6
HA
0.18 		1.6
HA
0.17 		1.6
C
0.2 		2
O
0.3 		1.4
NH1
0.32 		1.4
H
0.0074 		1.7
CT1
0.15 		2
HB
0.18 		1.6
CT3
0.17 		1.5
HA
0.15 		1.6
HA
0.1 		1.7
HA
0.13 		1.7
C
0.18 		2
O
0.25 		1.5
NH1
0.42 		1.4
H
0.026 		1.7
CT3
0.2 		1.5
HA
0.18 		1.6
HA
0.18 		1.6
HA
0.18 		1.6
Timing : wall: 0.23181[s] real, 0.08099[s] user, 0.15098[s] sys, run: 0.01307[s], integration: 0.00000[s], forces: 0.00000[s].