[gmx-users] reg Hydrophobic interaction

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 21 20:40:03 CEST 2011

vidhya sankar wrote:
> Dear Justin Thank you for your previous reply.
> As u mailed me already g_mindist  of gromacs is the best tool to study 
> about Hydrophobic contacts.
>  >From this i got only Average number of contacts. But i need the free 
> energy of Hydrophobic interaction  in energy units . I am  doing 
> umbrella pulling.
> Which Method is best to study Hydrophobic interaction energies

That sounds like an application for an MM/PBSA type calculation.  This is not 
something Gromacs can currently do, but you may be able to port your trajectory 
to other software that can.  I have no experience doing this; maybe someone else 
can comment.



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