R: [gmx-users] xtc corrupted during REMD

[Spitaleri Andrea]

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)

thanks a lot 


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
------------------------------------------------------------
________________________________________
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
> ------------------------------------------------------------
>
>
> -----------------------------------------------------------------------------------
> 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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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