[gmx-users] how to indicate solvent flexibility?
jalemkul at vt.edu
Tue Jan 8 18:15:58 CET 2013
On 1/8/13 11:42 AM, Albert wrote:
> I've finished a 60ns MD simulation with Gromacs and I found that the
> flixbility of solvent molecules inside the protein is different when it binds
> with different ligands: ie. in one case the solvent can move very fast with bulk
> environment, and in other case the solvent forms type Hbonds with resdiues
> inside protein. I am just wondering how which module of Gromacs can I use to
> indicate the solvent difference in flexibility? Is it possible to calculate the
> entropy in certain region (let's say: 20<Z<30 ) of the solvent?
It sounds like g_rmsf and g_msd may be useful here. The only way to specify
geometric criteria for index groups is to use g_select, but then the analysis
has to be done on each individual frame, not the trajectory. Dynamic selections
will be more conveniently implemented in a future Gromacs version.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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