[gmx-users] question about GBSA and opls-aa

Per Larsson per.larsson at sbc.su.se
Mon Feb 28 17:51:20 CET 2011


The treatment of 1-2, 1-3 and 1-4 interactions with gbsa differ between the different born radii models, but not between force fields.

For the Still model, polarisation energies are computed once for 1-2, 1-3 and 1-4 interactions, and never updated for these. For the HCT/OBC models, all interactions are included in the calculation of the born radii, and subsequently the polarisation energy, in every step. This is one of the reasons the Still model is faster, there are fewer calculations done per step.

There is thus no special scaling for these interactions in any force field when computing the polarisation energy. They all contribute.

For more details, please also read the original Still/HCT/OBC-papers.


28 feb 2011 kl. 16:51 skrev Baoqiang Cao <bqcaomail at gmail.com>:

> Hi,
> I'm using GBSA with opls-aa force field and have some questions that I
> couldn't find answers, I'd definitely be grateful if could get answer
> of tips. How does GBSA treat 1-2(covalent bonded), 1-3(bonded angle),
> 1-4(improper torsion) interactions? Should they all contribute nothing
> to GBSA energy or except 1-4?  Thanks in advance!
> Baoqiang
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