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

[vivek sharma]

Hi justin,

My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this issue
of running MD over a selected part of molecule.

With Thanks,
Vivek

2008/10/10 vivek sharma <viveksharma.iitb at gmail.com>

> 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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>
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