Re: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"

From: eprates_at_iqm.unicamp.br
Date: Mon Nov 04 2013 - 09:59:14 CST

Norman, yes, I am using GPUs. Does this interfere?

Erica

Quoting Norman Geist <norman.geist_at_uni-greifswald.de>:

> Are you using GPUs?
>
> Norman Geist.
>
>
>> -----Urspr√ľngliche Nachricht-----
>> Von: eprates_at_iqm.unicamp.br [mailto:eprates_at_iqm.unicamp.br]
>> Gesendet: Montag, 4. November 2013 15:43
>> An: Norman Geist
>> Cc: Namd Mailing List
>> Betreff: Re: AW: namd-l: Martini RBCG simulation frequently crashing
>> with "atoms moving too fast"
>>
>> Hi,
>>
>> Norman, I have already checked the beads and could not find any
>> problem. Actually, the identity of fast atoms vary each time the
>> simulation crashes.
>> The temperature I am using is 310 K. The simulation using ts = 5 fs
>> also crashed after 2319000 steps.
>>
>> Xavier, I will consider your suggestion, but I want to insist more in
>> NAMD, to which I am more used. Thanks.
>>
>>
>> Regards
>> Erica
>>
>>
>>
>>
>> Quoting Norman Geist <norman.geist_at_uni-greifswald.de>:
>>
>> > Did you try to find the mentioned beads visually, to check if they
>> > could be the problem? Make sure you didn't mix CG and non CG in your
>> > simulation. What temperature are you using?
>> >
>> > Norman Geist.
>> >
>> >
>> >> -----Urspr√ľngliche Nachricht-----
>> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> >> Auftrag von eprates_at_iqm.unicamp.br
>> >> Gesendet: Sonntag, 3. November 2013 18:57
>> >> An: namd-l_at_ks.uiuc.edu
>> >> Betreff: namd-l: Martini RBCG simulation frequently crashing with
>> >> "atoms moving too fast"
>> >>
>> >>
>> >> 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]
>> >> > #
>> >>
>> >
>> >
>> >
>> > Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica -
>> Unicamp
>> >
>> >
>>
>
>
>
> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
>
> !DSPAM:105,5277b6f171151605916098!

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