Quoting Mark Abraham <[EMAIL PROTECTED]>: > Justin A. Lemkul wrote: > > Quoting Mark Abraham <[EMAIL PROTECTED]>: > > > >> Itamar Kass wrote: > >>> Thank Justin, > >>> > >>> Still I am wondering about the grompp option, 'cause this is what I use > >>> most. You my also say I am invested in this (in CPU time manner). > >> You being cryptic doesn't serve your purpose of getting useful free help > >> :-) > >> > >> Justin's advice was correct but incomplete, in that grompp also has a > >> -time option you can use. The advice on the URL he provided will answer > >> both this and your other questions, as would reading the GROMACS manual > >> and/or man page :-) > > > > Thanks for pointing that out Mark, but I am wondering if you (or anyone > else out > > there) might be able to clear up a little confusion I have (and hence the > reason > > I have always used tpbconv if my .edr and .trr don't match up for whatever > > reason). Does the tinit option in the .mdp file override the -time > argument, > > in the same way that gen_vel = yes would override the velocity input from > the > > .trr? The manual and online documentation don't seem to give me a clear > answer > > to this question. > > I haven't tested that one... tinit overrides the time of the last > useable frame if you don't supply -time, so I'd have to suppose it works > the same way if the frame is specified with -time. If this were not > true, then tinit would be constrained to be a time in the supplied > trajectory. This kind of thing would be easy to check with some quick > changes to .mdp and/or command line and comparison of the output .tpr > with gmxcheck -s1 -s2. > > If you do this, please report what you see and I'll update the wiki page.
>From a quick test case, it appears that -time does not override what is specified in the .mdp file. For example, if tinit = 1000 in the .mdp file, but then I issue: $ grompp -f test.mdp -c conf.gro -p topol.top -t traj_1ns.trr -e ener_1ns.edr -time 500 -o test.tpr The output .tpr file starts at 1000 ps. So I suppose one would have to nix the tinit line in the .mdp in order to use -time. -Justin > > > I suppose it would be just as easy to remove any reference to tinit in the > .mdp, > > but in any case I'm curious. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
