From: PANAGIOTA KYRIAKOU (kyria008_at_gmail.com)
Date: Tue Dec 31 2013 - 11:28:12 CST
Hello,
I have been trying to equilibrate my system that consists of protein
embedded in a membrane and I get the following error:
*TIMING: 500000 CPU: 9750.65, 0.021551/step Wall: 9750.65, 0.021551/step,
0 hours remaining, 556.101562 MB of memory in use.*
*ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG*
*ENERGY: 500000 48376.8664 114689.7899 11643.7243
506.4399 -580965.4098 103191.7767 0.0000 246.2954
0.0000 -302310.5171 0.0000 -302310.5171
-302310.5171 0.0000 6488.4885 6928.4046
1914140.8650 6488.4885 6928.4046*
*WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000*
*WRITING COORDINATES TO DCD FILE AT STEP 500000*
*WRITING COORDINATES TO RESTART FILE AT STEP 500000*
*FINISHED WRITING RESTART COORDINATES*
*WRITING VELOCITIES TO RESTART FILE AT STEP 500000*
*FINISHED WRITING RESTART VELOCITIES*
*TCL: Writing to files with basename A_equil_1_min.*
*WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500000*
*WRITING COORDINATES TO OUTPUT FILE AT STEP 500000*
*WRITING VELOCITIES TO OUTPUT FILE AT STEP 500000*
*TCL: Running for 1000000 steps*
*REASSIGNING VELOCITIES AT STEP 500000 TO 303.15 KELVIN.*
*colvars: Writing the state file "A_equil_1.restart.colvars.state".*
*colvars: Synchronizing (emptying the buffer of) trajectory file
"A_equil_1.colvars.traj".*
*ERROR: Constraint failure in RATTLE algorithm for atom 6522!*
*ERROR: Constraint failure; simulation has become unstable.*
*ERROR: Constraint failure in RATTLE algorithm for atom 13834!*
*ERROR: Constraint failure; simulation has become unstable.*
*ERROR: Constraint failure in RATTLE algorithm for atom 1812!*
*ERROR: Constraint failure; simulation has become unstable.*
When I tried to fix it I realized that the Temperature increased from 0 to
312 K, instantly after minimization even though I am using temperature
reassignment. Here is my configuration file:
*#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
*# Custom variables*
*set temp 303.15 *
*# inputs*
* structure ../A.psf ; *
* coordinates ../A.pdb ;*
* paraTypeCharmm on*
* parameters ../../common/topology/par_all36_prot_nomass.prm*
* parameters ../../common/topology/par_all36_water_ions.prm *
* parameters ../../common/topology/par_all36_lipid.prm *
* temperature $temp ;*
* # simulation parameters*
* outputname A_equil_1 ;*
* outputEnergies 1000 ;*
* outputTiming 1000 ;*
* xstFreq 10000 ;*
* dcdFreq 10000 ;*
* dcdUnitCell yes *
* binaryoutput on ;*
* restartfreq 10000 ;*
* seed 1369948321 ;*
*# calculation parameters*
* exclude scaled1-4 ;*
* 1-4scaling 1.0 ;*
* switching on ;*
* switchDist 9 ;*
* cutoff 10 ;*
* pairlistdist 12 ; *
* stepsPerCycle 20 ;*
* rigidbonds all ;*
* vdwForceSwitching yes ;*
* timestep 1 ; *
* nonBondedFreq 1 ;*
* fullElectFrequency 1 ;*
* cellBasisVector1 139.65999603271484 00.00 00.00 ;*
* cellBasisVector2 00.00 140.35699462890625 00.00 ;*
* cellBasisVector3 00.00 00.00 97.64900207519531 ;*
* cellorigin -0.9953396916389465 4.457383155822754
2.071026086807251 ;*
* wrapAll on ;*
* wrapWater on ;*
* wrapNearest off ;*
*# PME*
* Pme on ;*
* PmeGridsizeX 144 ;*
* PmeGridsizeY 150 ;*
* PmeGridsizeZ 108 ;*
*# Control (need to be specified before runs) *
* useFlexibleCell yes ;*
* useGroupPressure yes ;*
* useConstantRatio yes ;*
*# constant pressure*
* langevinPiston on*
* langevinPistonTarget 1.01325*
* langevinPistonPeriod 50.0*
* langevinPistonDecay 25.0*
* langevinPistonTemp $temp*
* reassignFreq 1000 ;*
* reassignTemp 1 ;*
* reassignIncr 1 ;*
* reassignHold $temp ; *
* colvars on*
* colvarsConfig ../restraints/A_equil_1.col *
*#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
* # EXECUTION*
*#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
* minimize 500000*
* run 1000000*
Do you know what could have caused the increase in the temperature?
I would appreciate your help so much,
Giota
Panagiota Kyriakou
Graduate Student
Dept. of Chemical Engineering and Materials Science
University of Minnesota
email: kyria008_at_umn.edu
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