[gmx-users] xtc corrupted during REMD

[Mark Abraham]

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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