Hello:

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.

Reply via email to