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
--
========================================
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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