[gmx-users] picking out resident water molecule?

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 12 14:02:53 CET 2011

Yun Shi wrote:
> Hi everyone,
> I am doing MD simulation with a protein-ligand system, and I want to 
> pick out the water molecules (their residue numbers or coordinates in 
> any frame) that simultaneously contact (within 0.4 nm range for heavy 
> atoms) the ligand and the protein, so that I could plot the lifetime of 
> these resident water molecules within a trajectory.
> Does anyone know how to achieve this within GROMACS?

You can create the index group with g_select, but since the size of these groups 
is not guaranteed to be the same in each frame, there is not an automated way of 
calculating these quantities using the groups.  You could, in theory, use the 
index groups on each frame individually and reassemble the output data into a 
file that can be plotted.  It would be quite tedious, but certainly possible.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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