[gmx-users] Water near protein

X.Periole X.Periole at rug.nl
Tue May 9 23:24:37 CEST 2006

On Tue, 9 May 2006 16:48:43 -0500
  Ashutosh Jogalekar <ajogale at emory.edu> wrote:
> Hi
> I have a protein that I have simulated for 1 ns. I want 
>to observe  the variation in the number of water 
>molecules within 2.0 A of the  backbone of the protein, 
>as a function of time. So I should be able  to see this 
>variation as a graph in xmgrace, with time on the X axis, 
> and the number within 2.0 A on the Y axis. What command 
>could I use  for doing this? If not, is there any way 
>that this can be done?

g_mindist can counts the number of contacts between two
groups (protine and oxygen of water molecules in your 
within a given distance.

check g_mindist -h


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