[gmx-users] number of solvent molecule

[chris.neale at utoronto.ca]

> I went through the documentation of g_hbond, But I
> think it does not give me the number of solvent
> molecules present in a solvent shell arround my
> protein. I am able to calculate no. of contacts
> between protein and solvent but that is not equal to
> the no of molecule present. Is there any suggetion?
> regards
> Chiradip

Use g_rdf and integrate the radial distribution function to either
a)the first minimum
b)the first maximum and double the value
c)some predetermined cutoff value (like 0.6nm, athough that sounds a  
little large to be a single solvation shell).




>> Come to think of it, you can even skip the -contact
>> flag if you feel
>> like it. In any case, g_hbond is probably the way to
>> go. Have a look at
>> its documentation.
>>
>> /Erik
>>
>> On Tue, 2006-11-28 at 09:43 +0100, Erik Marklund
>> wrote:
>> > g_hbond -contact. But then again, that's my answer
>> to everything :-)
>> >
>> > Oh, and use (one of) the latest versions of
>> gromacs, otherwise the
>> > -contact option might not work properly.
>> >
>> > /Erik
>> >
>> > On Mon, 2006-11-27 at 21:14 +0000, chiradip
>> chatterjee wrote:
>> > > Hi gmxusers,
>> > > I am a new user of gromacs. I completed a MD run
>> of my
>> > > protein in a solvent box.
>> > > Now I want to calculate the number of solvent
>> > > molecules (molecules/cc) present arround a shell
>> of
>> > > 0.6nm from my protein (or sidechains).

>