Ok, thanks -- I see I will have to go back to version 4.5 or 4.6 where my code worked flawlessly (particle decomposition is available there).
Regarding "flying away" -- sometimes I NEED my system to disintegrate to fragments which fly away;) Momentum is of course conserved, cause they fly in opposite directions. Thank you for the links, I will have a look. With kind regards Jan 2015-06-14 19:32 GMT+02:00 V.V.Chaban <vvcha...@gmail.com>: > There are just two options for such simulations. Either one uses a > code supporting particle decomposition or adds a vacuum layer. > > The fragments will not fly away provided that momentum is conserved. > > Some comments on why and what to select may be present here: > > http://pubs.acs.org/doi/abs/10.1021/jz500563q > > http://pubs.acs.org/doi/abs/10.1021/jz300405q > > http://pubs.acs.org/doi/abs/10.1021/jz201190j > > > > > > > On Sun, Jun 14, 2015 at 2:24 PM, Jan Jirsák <janjir...@gmail.com> wrote: >> 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. -- 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.