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

From: eprates_at_iqm.unicamp.br
Date: Wed Nov 06 2013 - 11:17:19 CST

Norman,
Ok, I will test the GPUs and tell you what happened.
Thanks.
Erica

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

> I just think that one of your GPUs might be broken. The fact that
> the problem occurs so randomly, could be attributed to little errors
> that unload with huge impact due the large timestep. Therefore it
> works better for smaller timesteps and regular all-atom md. If
> nobody jumps in here to tell this is a known problem with the CG
> forcefield or whatever, the most likely reason IMHO is a broken GPU.
> Try to exclude specific GPUs to find out if one is doing the
> problems or try cudamemcheck.
>
> Norman Geist.
>
>> -----Ursprüngliche Nachricht-----
>> Von: eprates_at_iqm.unicamp.br [mailto:eprates_at_iqm.unicamp.br]
>> Gesendet: Montag, 4. November 2013 16:59
>> An: Norman Geist
>> Cc: Namd Mailing List
>> Betreff: Re: AW: AW: namd-l: Martini RBCG simulation frequently
>> crashing with "atoms moving too fast"
>>
>> 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.
>> >
>> >
>> >> -----Ursprüngliche 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.
>> >> >
>> >> >
>> >> >> -----Ursprüngliche 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
>> >
>> >
>>
>
>
>
> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
>
> !DSPAM:105,5278b4c171157800479760!

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