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: [email protected] [[email protected]] per conto di Mark Abraham [[email protected]] 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------------------------------------------- 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
