Hello everyone.
I am doing some simple tests as following: I have an amber crd and top file. I perform an energy evaluation and I estimate the value of BOND, ANGLE and TORSION energies for a simple system (ace-ala-nme).
Then I use amb2gmx.pl to convert the crd and top file to gromacs format and again I compute the BOND, ANGLE and TORSION energies of the same structure ...
I expect to have identical values between gromacs and amber. However, the energis are not comparable.
amber ... BOND= 0.0206 (kcal/mol) ANGLE=0.3620 (kcal/mol) TORSION=8.1071 (kcal/mol) gromacs .... BOND=0.14044 (kcal/mol) ANGLE=0.3780 (kcal/mol) TORSION=9.74190 (kcal/mol)
I checked how amb2gmx converted the values of amber to gmx format. It seems to me that everything is correct. There is a factor of two difference between the force constants in amber and gromacs which I think in the energy calculation term ... it is already taken care of!
So I see nothing wrong but ... energies dont match!
Could you please help me to understan this
Thanks
Golshan
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Received on Thu Aug 08 2013 - 12:30:03 PDT
