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 <[email protected]> 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 <[email protected]>: >> 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 <[email protected]> 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 <[email protected]>: >>>> 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 [email protected]. >> -- >> 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 [email protected]. -- 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 [email protected].
