Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> Jamie Seyed wrote: > >> Dear all, >> I have questions regarding the position restrain md. I tried to find the >> answer of my questions from the mailing list, but it is not clear yet. >> In the fws tutorial when it says (in the pr.mdp) >> tc_grps=Protein non-protein >> (1) Doesn't that mean everything in the system? I think for this case we >> can >> simply write "system" because system is made by protein and non-protein?? >> > > It includes the whole system, but it is often a good idea not to couple > groups of heterogeneous heat capacity to the same thermostat. That said, if > the groups are too small, you get other problems. See also > http://oldwiki.gromacs.org/index.php/temperature_coupling > > (2) In this case how program recognize which one should restrain and which >> one not, because it included all?? >> > > Temperature coupling has no linkage with position restraints. You defined > the latter in your .top file. > > (3) This step is required for every system or only proteins?? >> > > It may or may not be useful in achieving stable equilibration for any > system. See > http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation > > (4) If I want to make an index file and I specify a group that need to be >> constrained, in the generated index file I will get system and all its >> parts >> and an extra part for my specific part that need to be constrain...Is that >> ok?? >> > > "constraints" are different from "restraints" in GROMACS usage. make_ndx > does allow you to generate new index groups, but you will need to (re-)read > the relevant manual sections to understand that neither of these algorithms > uses index groups. (Or to prove my memory wrong!) > > (5) In my case I have a molecule (MOL) and water (SOL), for position >> restrain md should I use "tc_grps=MOL SOL" (according to fws tutorial) >> or >> I need only write "tc_grps=MOL"?? Many Thanks in Advance/Jamie >> > > The latter won't work, for all atoms must be members of a > temperature-coupling group if any are. > > What you actually need is a clear understanding of your strategic > objective. Hopefully some of the links will move you towards that. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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