Mark, THe normal mdrun also hangs thus not generating any output.
On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: > > Hi, > > Its going into the running mode but gets hang there for long hours which > generating any data in the output file. And am not able to figure out the > error file_doc. Please anyone knows what's going wrong. > > > No, but you should start trying to simplify what you're doing to see where > the problem lies. Does normal mdrun work? > > Mark > > > Thanks > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! > > -----Original Message----- > From: Szilárd Páll <szilard.p...@cbr.su.se> <szilard.p...@cbr.su.se> > Sender: gmx-users-boun...@gromacs.org > Date: Wed, 18 Jan 2012 14:47:59 > To: Discussion list for GROMACS users<gmx-users@gromacs.org> > <gmx-users@gromacs.org> > Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> > <gmx-users@gromacs.org> > Subject: Re: [gmx-users] mdrun-gpu error > > Hi, > > Most of those are just warnings, the only error I see there comes from > the shell, probably an error in your script. > > Cheers, > -- > Szilárd > > > > On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar<aiswarya.pa...@gmail.com> > <aiswarya.pa...@gmail.com> wrote: > > Hi users, > > Am running mdrun on gpu . I receive an error such as= > > WARNING: This run will generate roughly 38570 Mb of data > > > WARNING: OpenMM does not support leap-frog, will use velocity-verlet > integrator. > > > WARNING: OpenMM supports only Andersen thermostat with the > md/md-vv/md-vv-avek integrators. > > > WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. > > > WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and > CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" > option. > > /bin/cat: file_loc: No such file or directory > > > and the job is running but the nothing written into .xtc, .trr, .edr files . > What could have gone wrong? > > -- > Aiswarya B Pawar > > Bioinformatics Dept, > Indian Institute of Science > Bangalore > > > > -- > gmx-users mailing list > gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive > athttp://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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list > gmx-users@gromacs.orghttp://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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore
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