[gmx-users] xtc corrupted during REMD

[Spitaleri Andrea]

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). 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

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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)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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