From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 04 2013 - 09:02:04 CST
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
> >
> > !DSPAM:105,52774b8e71151528363982!
>
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