From: eprates_at_iqm.unicamp.br
Date: Sun Nov 03 2013 - 11:57:18 CST
Dear all,
I am running a Martini RBCG molecular dynamics simulation of a
protein of about 550 residues in water. I have, first, minmized the
system during 1000 steps. Then, the system have undergo a two phases
relaxation period, in which, in the first part, the whole protein is
frozen to don't move, while all the other atoms are free. In the
second part of the relaxation, only the backbone beads are frozen.
Subsequently, I have run the NPT simulation with 5 fs timestep,
during 200,000 steps, with all the atoms free to move. After that, I
have increased the timestep to 10 fs.
The problem I am facing is that the simulation is frequently getting crashed
with errors "atoms moving to fast", as the following:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 382000
WRITING COORDINATES TO DCD FILE AT STEP 382000
WRITING COORDINATES TO RESTART FILE AT STEP 382000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 382000
FINISHED WRITING RESTART VELOCITIES
LDB: ============= START OF LOAD BALANCING ============== 6755.22
LDB: ============== END OF LOAD BALANCING =============== 6755.22
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 6755.22
LDB: ============= START OF LOAD BALANCING ============== 6756.1
LDB: Largest compute 4049 load 0.000477 is 0.5% of average load 0.101946
LDB: Average compute 0.000058 is 0.1% of average load 0.101946
LDB: TIME 6756.1 LOAD: AVG 0.101946 MAX 0.131312 PROXIES: TOTAL 245
MAXPE 35 MAXPATCH 1 None MEM: 99.7734 MB
LDB: TIME 6756.1 LOAD: AVG 0.101946 MAX 0.131312 PROXIES: TOTAL 267
MAXPE 46 MAXPATCH 2 RefineTorusLB MEM: 99.7734 MB
LDB: TIME 6756.12 LOAD: AVG 0.101946 MAX 0.103445 PROXIES: TOTAL 272
MAXPE 48 MAXPATCH 2 RefineTorusLB MEM: 99.7734 MB
LDB: ============== END OF LOAD BALANCING =============== 6756.12
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 6756.12
ERROR: Atom 9646 velocity is -759.411 -118.145 -2502.89 (limit is
1200, atom 13 of 68 on patch 73 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms
on patch 73 pe 0).
ERROR: Exiting prematurely; see error messages above.
====================================================
WallClock: 6768.302246 CPUTime: 6768.302246 Memory: 99.773438 MB
Program finished.
With ts=10 fs, the simulation stands not longer than 382000 steps. I
have also tried to simulate using ts=8 fs, but the simulation also
crashed, after 1230000 steps. Now I set again ts=5 fs to see if I can
run during some hundreds of nanoseconds.
Anyway, I think this is a too short time step for a standard CG MD
simulation, isn't it?
Has anyone faced the same problem and could give me a hint about why
it is happening? I send the configuration file described bellow.
I appreciate any help.
Best regards,
Erica
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
> #NPT lipoprotien system
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> set inputname system-eq3
> set outputname system-din
> set restart 1
>
> set pvmode "p"
> set temode "t"
>
> proc get_first_ts { xscfile } {
> set fd [open $xscfile r]
> gets $fd
> gets $fd
> gets $fd line
> set ts [lindex $line 0]
> close $fd
> return $ts
> }
>
> set temperature 310
> cosAngles on
>
> structure cg-fixed.psf
> bincoordinates $inputname.coor
> coordinates cg-fixed.pdb
> extendedSystem $inputname.xsc
> binvelocities $inputname.vel
>
> # Nao entendi isso..
> #if {$restart == 1} {
> # bincoordinates $inputname.coor
> # binvelocities $inputname.vel
> # extendedSystem $inputname.xsc
> # svim urrenttimestep [get_first_ts $inputname.xsc]
> ## COMMotion yes
> #} else {
> # temperature $temperature
> # set currenttimestep 0
> #}
>
> # Do meu jeito
>
> #extendedsystem $inputname.xsc
> restartname $outputname
> firsttimestep 0
> #temperature $temperature
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters /home/erica/toppar/martini/martini-par/martini-protein-bonds.par
> parameters
> /home/erica/toppar/martini/martini-par/martini-protein-angles-cos.par
> parameters
> /home/erica/toppar/martini/martini-par/martini-protein-dihedrals.par
> parameters /home/erica/toppar/martini/martini-par/martini-all-nonb.par
> parameters
> /home/erica/toppar/martini/martini-par/martini-lipids-bonds-angles-dihedrals.par
>
> # Force-Field Parameters
> exclude 1-2
> 1-4scaling 1.0
> cutoff 12.0
> martiniSwitching on
> PME off
> switching on
> switchdist 9.0
> pairlistdist 14
> dielectric 15.0
>
>
> # Integrator Parameters
> timestep 10.0 #was 25
> nonbondedFreq 1
> stepspercycle 10
>
> #Constraints and restraints
>
> #if {0} {
> #constraints on
> #consref .pdb
> #conskfile .ref
> #conskcol B
> #}
>
> #if {0} {
> #fixedAtoms on
> #fixedAtomsFile file
> #fixedAtomsCol O
> #}
>
> #fixedAtoms on
> #fixedAtomsFile cg-fixed-fixedatoms-eq2.pdb
> #fixedAtomsCol B
>
> # Constant Temperature Control
> if {$temode == "t"} {
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient(gamma)5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
> }
>
>
> # Periodic Boundary Conditions
>
> #if {1} {
> #cellBasisVector1 106.0 0 0
> #cellBasisVector2 0 106.0 0
> #cellBasisVector3 0 0 106.0
> #cellOrigin 52.5 52.5 52.5
> #}
> wrapAll on
>
> #
> #PME yes
> #PMEGridSizeX 256
> #PMEGridSizeY 256
> #PMEGridSizeZ 256
>
>
> #margin 5.0
>
> # Constant Pressure Control (variable volume)
> useGroupPressure no # no hydrogens in CG hence set this to no
> inspite of 1 fs step
> #useFlexibleCell yes
> #useConstantArea no
> #useConstantRatio yes
>
> if {$pvmode == "p"} {
> langevinPiston yes
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> #one may need to bump up the pressure constants at first
> langevinPistonPeriod 2000. #usually 2000
> langevinPistonDecay 1000. #usually 1000
> langevinPistonTemp $temperature
> }
>
>
> # Output
> outputName $outputname
>
> restartfreq 1000
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
>
>
> # Minimization
> #if {$restart == 0} {
> #minimize 20000
> #reinitvels $temperature
> #}
>
> run 5000000
> #%set totsimtime 5000000
> #%run [expr $totsimtime - $currenttimestep]
> #
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