[gmx-users] solvent_protein interaction energy

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 1 15:17:36 CEST 2011

balaji nagarajan wrote:
> Thanks for the reply !
> I have tried building the topology with  generating the index file
> make_ndx  -f  * 
> it gave options i have selected the protein and the solvent

An index file is unnecessary for default groups.


> then i gave minimization
> in the minimization file i have included
> energygrps = Protein SOL ,
> but the energy file have the same when i removed and inserted the above 
> flag !
> if any one can explain me in detail it will be helpfull

EM is a poor choice for testing; not all options designed to work with MD 
integrators are incorporated in simple EM procedures, although I do not see why 
(in this case) it shouldn't work.  A better test is a zero-step MD run (md 
integrator).  Note that not all terms are decomposable pairwise, just 
short-range nonbonded terms.



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


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