On 05/03/11, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > > Moeed wrote: > >Hello, > > > >I am attempting to increase the density using NPT. As I increase the > >pressure to compress the system after some steps simulation crashes. I > >thought maybe its becasue I am compressing too fast but even when I take a > >stepwise approach to compress gradually the same error comes up. The density > >at the point of crash is about 30 SI while I need 650 which is the actual > >density. Topology file is generated successfully and also I did EM before MD. > > > >Initial box size is 30 nm. As suggested in the link below I reduced the size > >to 20 nm (there are 2500 atoms in the system ) but the same error appears. > >http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html > > > >I also tried less -np from 7 to 4 but no success. > > > >Can you please tell me what this exclamation mark mean which I get at times > >in parallel trials.(vol 0.99 !) > > > > Domain decomposition relies on dividing your system up into reliably-sized > domains in order to communicate force, coordinate, energy, etc. information. > If something happens to skew or annihilate these domains, the algorithm > crashes. The exclamation marks indicate (in a general sense) that the DD > algorithm has detected something dangerously wrong. > > If you're trying to make drastic changes to the size or dimensions of your > system, DD is a bad choice and you'll likely have to use particle > decomposition (mdrun -pd). >
Or during compression, do regular and frequent grompp -t .trr -e .edr restarts so that the DD information in the checkpoint file is not propagated, and so you can do a new DD based on the current volume. Mark > > > <snip> > > >fourierspacing = 0.3 > > You're setting yourself up for inaccurate PME calculations with this. Use > 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > >
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