[gmx-users] Water near protein

[Mark Abraham]

Ashutosh Jogalekar 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?

Please read the descriptions of the utility programs in the gromacs 
manual. If one of those sounds like it does the job, go ahead and try 
it. Otherwise, look around at other tools (I don't know of any, others 
on here might), or write your own.

Mark