[gmx-users] Barostat relaxation times
UNRESTRICTED / ILLIMITÉE Dear Gromacs users, Does anyone have any advice on how to choose an appropriate barostat relaxation time? I'm quite new to molecular dynamics, and I am running some simple simulations of a box of water using a Nose-Hoover thermostat, a Parrinello-Rahman barostat, and several different flexible water models. I've been looking online and in the literature for some guidance on how to appropriately choose the barostat relaxation time, but what I've found so far is somewhat conflicting (partially due to wide differences in applications). Does anyone have advice on choosing a barostat relaxation time for a flexible water system, or perhaps an idea of a reference on the subject? Also, what is the minimum amount of time that a system like this should be equilibrated before performing a production run? Thanks, Katy -- 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.
[gmx-users] Steps in the velocity autocorrelation function
UNRESTRICTED / ILLIMITÉE Dear GROMACs users, Why does the velocity autocorrelation function generated by gmx velacc have vertical steps in it (e.g. multiple entries for the same time)? Thanks, Katy -- 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.
[gmx-users] Documentation of gmx velacc spectrum and gmx dos
UNRESTRICTED / ILLIMITÉE Dear GROMACS users, I am new to GROMACS, and I was wondering whether someone could direct me to documentation on exactly what is calculated in the spectrum option (-os) of gmx velacc, as well as the gmx dos function? They don't seem to be documented in the reference manual, and I'm not sure how to deal with the use of arbitrary units. Thanks, Katy -- 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.
[gmx-users] nMoldyn with GROMACS
UNRESTRICTED / ILLIMITÉE Dear GROMACS users, Does anyone have experience using nMoldyn with GROMACS output? If so, could you please let me know how you converted the GROMACS trajectory to MMTK format? I would like to use nMoldyn to analyse trajectories output by GROMACS. I have converted the GROMACS trajectory output to .dcd format using Wordom, and have tried using the NAMD and CHARMM conversion options in nMoldyn to convert to the appropriate MMTK format. The conversions claim to be successful, but when I load the generated .nc file it seems that the periodic boundary conditions of my system have been lost (nMoldyn recognises an infinite universe). Further analysis operations with nMoldyn don't work properly either. I am not sure whether the problem is occurring in the Wordom conversion or in the nMoldyn conversion step (although I am guessing that the Wordom-generated .dcd file is not in the right format for either nMoldyn conversion option). Thanks very much, Katy -- 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.
