[gmx-users] how to run production MD for only a fragment of protein

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 2 17:40:32 CEST 2012

On 6/2/12 11:33 AM, Acoot Brett wrote:
> Dear All,
> Can you tell me a web link on a protocol or reference for steered production MD
> or the production MD just for only a fragment of the whole protein, by GROMACS?

That's sort of a broad request.  If you can describe more specifically what you 
want to do, you're more likely to get some assistance.  There are tons of 
literature references about modeling peptide fragments.  For other web links or 
tutorials, a few minutes on the Gromacs website and Google will tell you if such 
instructions exist.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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