[gmx-users] Electrostatic interactions between residues

[Justin A. Lemkul]

Carla Jamous wrote:
> Hi everyone,
> 
> please is there a way to know if electrostatic interactions exist 
> between my ligand and my protein during the trajectory? Which tool can I 
> use for this purpose, other than g_saltbr?

You can quantify short-range nonbonded energies using energygrps, which at this 
point would require using the -rerun feature of mdrun.  You can also get a list 
of contacts using g_mindist and/or g_dist, as well as distance matrices with 
g_mdmat.

-Justin

> 
> Thank you,
> Carla
> 

-- 
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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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