Dear Mijiddorj, We have had good energy conservation with bond constraints and a 1 fs time step under double precision, using a setup similar to yours. We did not remove rotation however, because we wanted to honour the rotational temperature of the system. Whether that is an important choice or not is for you to decide, but do note that the spinning ice cube effect is an artefact arising from the thermostat, which is turned off in your setup.
Whether bonds should be constrained or not is related to what your scientific questions are, and the time step depends on what bonds are constrained, if any. I can’t remember what LINCS parameters we used, but be prepared to increase the order and/or iter. Consult the manual for details. Kind regards, Erik ______________________________ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 20 Jan 2017, at 11:01, Мижээ Батсайхан <b.mijidd...@gmail.com<mailto:b.mijidd...@gmail.com>> wrote: Dear gmx users, I would like to get experience of simulation in vacuum. Please suggest me tutorials, and advice me. I read about following comments which written on Shourjiya Sanyal tutorial. Can you discuss about it? In vacuum simulation, integration should be reduced compared to solvent phase simulation. Periodic boundary conditions, non-bonded interaction cutoffs, temperature coupling and pressure coupling were all turned off. Center of mass translation and rotation around the center of mass are to be removed to avoid the fast spin of the protein. One should also constrain the hydrogen bond using algorithms like SHAKE/LINCS. http://www.shourjya.thinkbiosolution.com/md-simulation-in-gas-phasevacuum-with-gromacs/ Best regards, Mijiddorj -- 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.
