[gmx-users] comparing gmx GB energy with Amber11

Sandeep Somani ssomani at gmail.com
Thu Nov 8 05:43:50 CET 2012


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

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
{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


Wales Group

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