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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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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