[gmx-users] how to indicate solvent flexibility?

[Leandro Bortot]

     My first thought was to compare the diffusion of the bulk and internal
waters with g_msd.

     You said that in some case the internal waters forms hydrogen bonds
with the protein. I think that in this case a plot showing this would be
nice too.


2013/1/8 Justin Lemkul <jalemkul at vt.edu>

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