[gmx-users] Re: gmx-users Digest, Vol 25, Issue 5

gil claudio gilclaudio at yahoo.com
Thu May 4 04:19:28 CEST 2006

Thanks for the help, Erik and David.

Does this mean that when invoking rb dihedrals, the
real equation being used is

RB(phi) = C0 - C1 cos(phi) + C2 cos^2(phi) - C3
cos^3(phi) + C4 cos^4(phi) - C5 cos^5(phi)

It might be good to mention this convention in the

Message: 3
Date: Tue, 2 May 2006 11:45:27 +0200
From: Erik Lindahl <lindahl at sbc.su.se>
Subject: Re: [gmx-users] correction in oplsaa to rb
To: Discussion list for GROMACS users
<gmx-users at gromacs.org>
<6FD5AC18-9E24-4B89-9901-DB0C7E95197A at sbc.su.se>
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On May 2, 2006, at 9:48 AM, David van der Spoel wrote:

> gil claudio wrote:
>> I just derived the conversion of the dihedral
>> constants from OPLSAA to RB and I get a set of
>> equations different from the ones printed in the
>> manual (3.3, p 56).
>> C1 = V1 / 2 - 3 V3 / 2
>> C3 = 2 V3
>> These are the negative of what is printed in the
>> manual.
> I think you're right. Question now is what was used
in the  
> derivation of the parameters? Erik, can you comment?

The equations in the manual are correct, although I
did rederive  
everything from scratch during the first port.

I bet both of you are forgetting the conversion
between polymer and  
biochemistry convention. That will give you a minus
sign for all odd  
powers of cos(phi).

> Also the reference (60) is incorrect, it should be
> Jorgensen, J. Phys. Chem. 90 (1986) 1276
> Finally, do also note that in the latest OPLS paper
> Jorgensen & Tirado-Rives J. Comp. Chem. 26 (2005)
> a further term is introduced in the torsion
function. This is not  
> yet used in GROMACS AFAIK.

It was present already in the 2001 OPLS-AA/L paper,
and we do use it,  
although only for a handful of torsions.

The 2005 paper is only a summary/presentation of MCPRO
and BOSS as  
far as I know - no new data for the force field.



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