[gmx-users] Accounting for the solvent with -rerun?

Leandro Bortot leandro.obt at gmail.com
Thu Jul 11 22:55:05 CEST 2013

Dear users,

     I ran a "common MD simulation" of a solvated protein and, from the
full .trr, I extracted only the protein trajectory with trjconv, no solvent
nor ions. Similarly, I used the same original .tpr with tpbconv to get a
.tpr which corresponds only to the protein. I used mdrun -rerun with the
protein's tpr and trr and finally I got the potential energy from the
"recalculated" .edr file.

     Am I right when thinking that, because there is no solvent in this new
.trr, the potential energy was calculated in vaccum? If I am right, do you
think that using a new .tpr with Implicit Solvent would be a good option
for recalculating this energy with the protein's trr?
     My interest is exactly to know how the energy of the protein behaves
during the simulation. I plan to calculate the interaction energy between
two proteins by doing such trajectory decompositions and energy

Thank you in advance,
Leandro Bortot

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