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
On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham <mark.abra...@anu.edu.au>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 <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 >>> >>> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > _______________________________________________ > 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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