Hi Justin, Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did something wrong? Is it always the same order for different systems? Can you please give me some advice about it?? Many Thanks in Advance/ Jamie
On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Hi, >> How can I make sure that position restraint is actually applied (after >> grompp & mdrun)? When I grep "POSRES" or "posres" I can not see any >> information... Many Thanks in Advance/Jamie >> >> > If your topology has the appropriate #ifdef POSRES, and you have "define = > -DPOSRES" in your .mdp file, then it worked :) Position restraints are > applied during mdrun, and show up in the .log file as "Position Rest." > entries. > > -Justin > > On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham > <[email protected]<mailto: >> [email protected]>> wrote: >> >> Jamie Seyed wrote: >> >> 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 >> >> >> pdb2gmx automatically produces a posre.itp file, whose position >> restraint contents are #included from the .top file it produces, and >> whose function is sensitive to the -DPOSRES option. Search the wiki >> for discussion of this machinery. >> >> Mark >> >> On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham >> <[email protected] <mailto:[email protected]>>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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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