[gmx-users] Calculation of water density around certain protein residues

[Dallas Warren]

You have a number of molecules, you know what those molecules are, you can calculate their mass, you know the volume, therefore you can calculate a density.  For the average for entire simulation, simply pass the water.xvg file to g_analyze

There is all the information you require right there in what you have already.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of bharat gupta
> Sent: Monday, 4 November 2013 10:33 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Calculation of water density around certain
> protein residues
> 
> Hi,
> 
> I want to know the exact way to calculate the density of water around
> certain residues in my protein. I tried to calculate this by using
> g_select, with the following command :-
> 
> g_select -f nvt.trr -s nvt.tpr -select "Nearby water" resname SOL and
> within 0.5 of resnr 115 to 118 -os water.xvg
> 
> In the output, I got for each time step I some number of residues. For
> eg,
> 
> @ s0 legend "Nearby water"
>       0.000  159.000
>       0.200  168.000
>       0.400  173.000
>       0.600  171.000
> 
> Can I get the average the number of water moleculed for the entire
> simulation time ?? and how can I get the density instead of number ??
> 
> 
> Pls respond to this query ...
> 
> Thanks
> ------
> Bharat
> --
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