[gmx-users] Position Restrain md
Jamie Seyed
jamie.seyed at gmail.com
Sun Aug 16 02:29:45 CEST 2009
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 <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>> 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>>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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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