[gmx-users] reg Hydrophobic interaction

[Justin A. Lemkul]

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

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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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