[gmx-users] MM-GB/SA analysis in Gromacs

Anna Marabotti amarabotti at unisa.it
Thu Nov 29 10:42:56 CET 2012

Dear gmx-users,

I ran several MD simulations using Gromacs 4.5.4 version, and now I'd 
need to calculate binding free energies using the MM-GBSA method. I 
searched through the manual and through the gmx-users archive, but I 
didn't find a way to do it. I found an old post in which it appeared 
that in the version 4.5 this possibility would have been available 
but it seems to me that this kind of analysis has not been implemented yet.
In another more recent post, I see that somebody has used mdrun -rerun 
in order to perform calculations, but I don't understand the correct 
procedure to use (apart from the suggestion of using .trr instead of 
.xtc files in order to avoid errors).

Does anyone have suggestions in order to do this analysis with Gromacs 
trajectories, before I make these calculations with another program?

Many thanks in advance and best regards

Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype: annam1972

"When a man with a gun meets a man with a pen, the man with the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)

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