And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message!
Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 19/01/2012 8:45 PM, aiswarya pawar wrote: > > Mark, > > THe normal mdrun also hangs thus not generating any output. > > > OK. It's your problem to solve... keep simplifying stuff until you can > isolate a small number of possible causes. Top of the list is file system > availability. > > Mark > > > > 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> >> Sender: gmx-users-boun...@gromacs.org >> Date: Wed, 18 Jan 2012 14:47:59 >> To: Discussion list for GROMACS users<gmx-users@gromacs.org> >> Reply-To: Discussion list for GROMACS users <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> 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.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 >> >> -- >> 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 >> >> >> >> >> >> -- >> 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 > > > > > > > -- > 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 -- 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
