[gmx-users] Position Restrain md

[Jamie Seyed]

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.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
>> >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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>>
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