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

[Justin A. Lemkul]

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

========================================