On Fri, Aug 09, 2013, Golshan Hejazi wrote:
>
> I computed the BOND and ANGLE energies. But it is only increasing my
> confusion ... Look: I have a simple ace-ala-nme system.
How about going to just ace-nme? It would much easier to compare each
individual term, and you would still have bonds, angles and dihedrals.
While I am thinking about it, be sure that the conversion of the blocking
groups (ace and nme) between Amber and Gromacs is correct (i.e. not just
the amino acids themselves.)
...dac
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Received on Fri Aug 09 2013 - 07:00:04 PDT
