Thank you for a reply - I could try that when everything else fails, but (i) my system can disintegrate and its fragments can fly really long distances apart, so the layer of vacuum would have to be considerably (and unpredictably) thick - the same applies to cutoffs, (ii) in principle I don't see why one should bother with periodic images in a simulation which is inherently non-periodic. Regards, Jan
2015-06-14 19:01 GMT+02:00 V.V.Chaban <vvcha...@gmail.com>: > Why don't you simply surround your molecule with a layer of vacuum and > use all periodic set of details as normally? This is what people do in > the plane-wave codes when the so-called 'cluster representation' is > desired. > > > > > On Sun, Jun 14, 2015 at 1:54 PM, Jan Jirsák <janjir...@gmail.com> wrote: >> Hi, >> >> I did the test and found out that -nt 8 is even slower than -nt 1 !! >> However, I think that simulation hasn't even properly started with 8 >> threads and got stuck somewhere in the beginning. >> >> Details: >> I used a short run (1000 steps) for testing. mdrun -nt 1 finished >> after ca 11 hours, whereas not a single checkpoint or run log record >> have been saved for mdrun -nt 8 (and simulation is still running). Not >> even starting energies were displayed - last record in a log file is a >> SETTLE citation. >> >> In top I noticed both processes used up to 100% CPU, but considerably >> differed in the use of memory. Relevant lines: >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 117710 jan 20 0 5313776 4.642g 9940 R 98.9 3.7 52:47.19 >> mdrun >> 117686 jan 20 0 547344 24456 8712 R 92.7 0.0 54:48.92 mdrun >> >> The first listed process (117710) is the single thread simulation (-nt 1). >> >> Thank you for any insight, >> Jan >> >> 2015-06-12 14:35 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: >>> Hi, >>> >>> Top need not be indicative. Run the same with -nt 1 and observe whether the >>> performance changes. And don't run anything else on these cores. >>> >>> Mark >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.