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.war...@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-boun...@gromacs.org [mailto:gmx-users-
boun...@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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