[gmx-users] Selection of water molecules

[Soham Sarkar]

For doing that you first tag only those water molecules which are within
0.5nm of the protein surface throughout the trajectory. To do it you need
to write a small python script using common_member option. And make an
index file only with those water molecules and calculate the rdf.

On Wed, 28 Aug 2019, 2:45 pm anupama sharma, <anusharma.jan1995 at gmail.com>
wrote:

> Dear users,
> I have to calculate the Pair Distribution Function of water present in my
> system near protein surface at 5 angstorm region for which I already did
> the indexing using gmx select (dynamic indexing). But when I tried to
> calculate the Pair Distribution Function using gmx rdf, I am getting option
> as to select the reference "the atoms present in one frame", not the
> atom/molecule for the system within a defined region and hence, I am unable
> to calculate the RDF of water molecule within a defined region for the
> whole trajectory which I want to do. Is there any possibility in gromacs to
> do so. I'll highly greatful if any one can help.
>
> Thanks in advance
> With regards,
> Anupama
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