[gmx-users] Running MD only for selected part of molecule

[vivek sharma]

hI justin,

Thanks for your response.
do I need to specify the index file(for residue that I want to keep fix
during MD) during GROMPP or just including the psre.itp in topology is
enough for the purpose ?

With Thanks,
Vivek

2008/10/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> vivek sharma wrote:
>>
>>> Thanks Justin,
>>>
>>> My goal is to keep certain part fixed and move only a few of the residues
>>> (case is like providing flexibility to the site of interest only).
>>> SO , do I need to specify the residue using some index file ?
>>> or is  there some other way to specify the part of molecule for position
>>> restraining ??
>>>
>>>
> Make an index file with the residues you want to keep fixed, and pass it
> to genpr to generate a new posre.itp that corresponds to those residues.
>
> -Justin
>
>
>>> With Thanks,
>>> Vivek
>>>
>>>
>>> 2008/10/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>>
>>>
>>>
>>>    vivek sharma wrote:
>>>
>>>        Hi there,
>>>         I want to run MD over a part of my molecule , for few residues
>>>        only (not the whole molecule).
>>>        Can I do it using GROMACS ?
>>>        I searched for the online documentation and mailing list, but
>>>        unable to get appropriate information.
>>>        If somebody has already tried such things earlier, please
>>>        suggest and direct me for appropriate link and address.
>>>
>>>
>>>    Well, if your goal is to keep certain parts fixed and allow others
>>>    to move, probably the easiest way to do it is to apply position
>>>    restraints to the "fixed" part.
>>>
>>>    -Justin
>>>
>>>        With Thanks,
>>>        Vivek
>>>
>>>
>>>
>>>  ------------------------------------------------------------------------
>>>
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>>>
>>>    --     ========================================
>>>
>>>    Justin A. Lemkul
>>>    Graduate Research Assistant
>>>    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
> Graduate Research Assistant
> 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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