[gmx-users] Electrostatic interaction Vs Z axis

[Justin A. Lemkul]

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.

-Justin

> Thanks in advance,
> -- 
> Aswathy
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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