[gmx-users] Electrostatic interactions between residues

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 27 15:00:05 CEST 2010

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 


> Thank you,
> Carla


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


More information about the gromacs.org_gmx-users mailing list