[gmx-users] xtc corrupted during REMD
andrea spitaleri
spitaleri.andrea at hsr.it
Mon Nov 22 09:11:17 CET 2010
Hi,
two on five have magic error at the same time. The simulation ends fine. Just the xtc files are
corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same
behavior (at different time) after the continuing run. First time, I suspected for some I/O error,
but now it sounds a bit strange. I will ask for a long simulation 50ns without extending steps.
thanks in advance
regards
and
On 11/22/2010 05:44 AM, Roland Schulz wrote:
>
>
> On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
> <spitaleri.andrea at hsr.it <mailto:spitaleri.andrea at hsr.it>> wrote:
>
> Hi,
> yes sure. Basically I do:
>
> 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 -> i get the
> first 5x25ns of remd simulation (five xtc every 5ps and five trr
> every 20ps, for each replica). I check those files by gmxcheck and
> they are fine. no errors.
>
> 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 25000000 -o
> runB_$i -> extension the simulation to 50ns total
>
> 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ ->
> at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted
> (from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns.
>
> >From the log file I do not see any errors. Everything seems fine.
> I have free room space in the hd too :)
>
> I am just wondering whether the problem is in the xtc options
> (precision and writing step)
>
>
> I doubt it that it has anything to do with your xtc options.
>
> Are all you xtc corrupted or only some? Are those which are corrupted
> all corrupted on the same frame or different ones?
>
> Roland
>
>
> ------------------------------------------------------------
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> Center of Genomics, BioInformatics and BioStatistics
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> http://sites.google.com/site/andreaspitaleri/
> Tel: 0039-0226434348/5622/3497/4922
> Fax: 0039-0226434153
> ------------------------------------------------------------
> ________________________________________
> Da: gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] per conto di Mark Abraham
> [Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>]
> Inviato: domenica 21 novembre 2010 17.03
> A: Discussion list for GROMACS users
> Oggetto: Re: [gmx-users] xtc corrupted during REMD
>
> On 21/11/2010 2:34 AM, Spitaleri Andrea wrote:
> > Hi there,
> > I am encountering a weird problem with a REMD simulation using
> 4.5.3. The total simulation is 50ns with 5 replica, and I do in two
> runs: 25ns and then continuing to 50ns (walltime queue). The first
> run is okay, the continue run (the last 25ns) randomly make some xtc
> files corrupted (from gmxcheck I get the Magic Number Error).
>
> I don't understand how the simulation can continue writing the .xtc
> files when you are getting magic number errors from gmxcheck. We need to
> see command lines for your workflow, please :-)
>
> Mark
>
> > It is strange since the respective trr files are okay and the
> simulation is still going (it is not blowing up from the log, not
> step.pdb files, not crash). The only difference is that I am writing
> the xtc often respect to the trr file and just the complex not the
> solvent:
> >
> > nstxout = 10000 ; coordinates every 20ps
> > nstvout = 0 ; velocity every 0ps
> > nstfout = 0 ; forces every 0 ps
> > nstlog = 2500 ; energies log every 5ps
> > nstenergy = 2500 ; energies every 5ps
> > nstxtcout = 2500 ; coordinates every 5ps to xtc
> > xtc-precision = 2500 ;
> > xtc-grps = complex;
> >
> >
> > Since the error is happening only for the continuing run, I am
> just wondering if there is any reason for this.
> >
> > thanks for any help
> >
> >
> > and
> >
> > ------------------------------------------------------------
> > Andrea Spitaleri PhD
> > Dulbecco Telethon Institute
> > Center of Genomics, BioInformatics and BioStatistics
> > c/o DIBIT Scientific Institute
> > Biomolecular NMR, 1B4
> > Via Olgettina 58
> > 20132 Milano (Italy)
> > http://sites.google.com/site/andreaspitaleri/
> > Tel: 0039-0226434348/5622/3497/4922
> > Fax: 0039-0226434153
> > ------------------------------------------------------------
> >
> >
> >
> -----------------------------------------------------------------------------------
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--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linkedin.com/in/andreaspitaleri
-------------------------------
-----------------------------------------------------------------------------------
SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE.
NON C'E' CURA SENZA RICERCA.
Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele.
Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org
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