[gmx-users] xtc corrupted during REMD

[Roland Schulz]

On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
<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 [gmx-users-bounces at gromacs.org] per
> conto di Mark Abraham [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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