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

[vivek sharma]

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 ??


With Thanks,
Vivek


2008/10/10 Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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