[gmx-users] Electrostatic interaction Vs Z axis

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 19 13:00:49 CEST 2010

Several messages that I sent yesterday look like they never made it to the list, 
for some reason.  Sorry if this is a double-post, just trying to get the reply 
out there...

Aswathy wrote:
> Dear Gromacs users,
> I want to find the electrostatic interaction energy between ligand and 
> protein, water and ligand during SMD of the ligand through the channel. 
> I have used g_energy but, I need to plot the energy against Z axis of 
> the channel.
> Could you please help me.

Use g_traj to extract the z-coordinate of the ligand, then you can plot energy
vs. coordinate.


> Thanks in advance,
> -- 
> Aswathy


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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