[gmx-users] Position Restrain md
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 16 02:39:05 CEST 2009
Jamie Seyed wrote:
> 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
>
I don't know anything about your system, so it's hard to make a generalization.
Positive values of potential indicate repulsive or unsatisfied interactions.
If you're running your system in solvent, I would think something is wrong;
vacuum might be a different story, but I don't usually do vacuum simulations, so
I don't have any real expertise here.
-Justin
> On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
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
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