[AMBER-Developers] Origin of dihedral term

From: Ross Walker <rosscwalker.gmail.com>
Date: Mon, 19 Oct 2015 15:25:00 -0700

Hi All,

I am wondering if anyone knows the origin or why the dihedral term we use in the AMBER force field has the 1+ term in it.

I.e. we have:

ndih n[i]
sum sum( 1/2 x Vn(1+cos(n.theta - phi)) )
i=1 j=1

Specifically we have the 1+cos term in there which is I guess to make the cos term oscillate between 0 and 2 rather than -1 and +1 and then we have the 1/2 in front of the Vn to get rid of the 2 making it between 0 and Vn. However, as far as I can tell this is purely cosmetic. Is that correct?

As in I could ditch the 1/2, and ditch the 1+ and just have V[i,j].cos(n.theta-phi). The question is if that is true why don't we do this - does anyone know?

The issue arrises not in MD but when we try and refit the torsion terms. If we try to fit energies against quantum energies we always have an offset in the mean due to the origins not matching - that doesn't matter since it would be constant during an MD run. However, if we are fitting Vn terms the 1+cos term here causes our mean to drift as we adjust Vn. This is a pain in the butt when it comes to getting a good fit. Thus I propose to just fit: Vn.cos(n.theta-phi) which, I believe would give perfectly transferable parameters to the 1+cos equation.

Am I missing anything here? - Is there any reason why we couldn't go the whole step and just ditch the 1/2 and 1+ terms from the entire force field? - Seems to me all that would happen is for a given set of parameters (say FF14SB) we just shift the energy origin but everything else would still work.

Comments welcome.

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |

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Received on Mon Oct 19 2015 - 15:30:02 PDT
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