[gmx-users] about potential energy calculation
mailmd2011 at gmail.com
Fri Jan 13 09:30:55 CET 2017
I submitted MD simulation for two small peptides with Amber FF. I
calculated the average potential energy of the system:
peptide A: -9x10^4 kcal/mol
peptide B: -6X10^4 kcal/mol
it seems that peptide A is more stable than B.
However, if I extract each frame the peptide from MD simulation and
submitted to energy minimization, the results is different:
peptide A: -180 kcal/mol
peptide B: -230 kcal/mol
In this case, peptide B is more stable than A.
I am just wondering why the calculations of the two cases are different?
Which one is reliable?
Thanks a lot
More information about the gromacs.org_gmx-users