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 manual. Message: 3 Date: Tue, 2 May 2006 11:45:27 +0200 From: Erik Lindahl <[EMAIL PROTECTED]> Subject: Re: [gmx-users] correction in oplsaa to rb conversion? To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, 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) 1689 > 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. Cheers, Erik __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
