[gmx-users] Position Restrain md
Mark.Abraham at anu.edu.au
Sat Aug 15 03:07:13 CEST 2009
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.
> On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham <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
>>> 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
>> (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
>> (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
>>> and an extra part for my specific part that need to be constrain...Is that
>> "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)
>>> 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.
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