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

From: eprates_at_iqm.unicamp.br
Date: Mon Nov 04 2013 - 08:42:53 CST

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]
>> > #
>>
>
>
>
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