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

[bharat gupta]

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