Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to replicate Amber's "igb=5 + large cutoff" in gmx.
According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
paper]".
I translated this to the following mdp options:
----
implicit_solvent = GBSA
gb_algorithm = OBC
All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of the
molecule.
{gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma,
gb_dielectric_offset} = corresponding Amber input.
----
Is that correct?
I realize that this is as much a question for Amber mailing list, but
trying here first! Any idea?
The molecule is ala-12. I'll be happy to send input files.
Thanks in advance
Sandeep
--
Postdoc
Wales Group
Cambridge
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