[gmx-users] how to indicate solvent flexibility?

Justin Lemkul jalemkul at vt.edu
Tue Jan 8 18:15:58 CET 2013

On 1/8/13 11:42 AM, Albert wrote:
> hello:
>    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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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