[gmx-users] solvent_protein interaction energy

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Default_Index_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

-- 
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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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