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
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.