[gmx-users] Freezing group

[Justin Lemkul]

On 3/28/13 4:24 PM, Алексей Раевский wrote:
> Hi dear All!
> Good day dear forum! I have a question abour freezing of atoms during MD.
> The idea is that - I have a protein and one domain contains a site. Also I
> have two ligands, one of them is better inhibitor in comparison with
> another one. To prepare the topology of the inhibitor I need to use a
> R.E.D.III server. As there are several different fitting methods, so I have
> to carry out a series of short MDs (about 5-10 ns) for each of them. The
> question is - is it possible to isolate this domain and fix/freeze last
> residues of the hairpin/linker to prevent movement of domain segments? I
> know that this is not the way to study ligand-protein interaction, however
> I just want to use it for understanding which topology generation method is
> better.

You can freeze whatever group you want using freezegrps and a custom index 
group.  It is also reasonably simple to restrain a segment of the structure 
using normal position restraints (again, created with a custom index group).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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