[gmx-users] Water near protein
Mark.Abraham at anu.edu.au
Wed May 10 01:49:37 CEST 2006
Ashutosh Jogalekar wrote:
> 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.
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