[gmx-users] torsion potential with 7 parameters

[Ángel Piñeiro]

Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals? 

Angel Pineiro.


> > Date: Tue, 29 Jan 2008 19:18:20 +0100
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] torsion potential with 7 parameters
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <479F6DEC.8000504 at xray.bmc.uu.se>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> > 
> > ngel Pieiro wrote:
> > > Hi all,
> > > anyone knows how to use (in gromacs) a potential of the type:
> > > 
> > > U_tors(phi_ijkl) = Sum_n 1/2 k_n [1-cos(n phi_ijkl)]
> > > 
> > > with n going from 1 to 7?
> > > 
> > > as far as I saw only the Ryckaert-Bellemans with 6 parameters and a
> > > periodic function are implemented in gromacs. Chapter 4 says something
> > > about this subject and it explains how to translate OPLS in R-B but it
> > > seems that 7 parameters are not included
> > > 
> > > I am trying to use the force field for perfluoroalkanes published by
> > > Borodin et al in JPCB (106) 2002, 9912.
> > 
> > 
> > in the worst case you can add two dihedrals, however n = 6,7 is not 
> > implemented. you can however tabulate this if I'm not mistaken.
> > 
> > > Thanks in advance for the help,
> > > 
> > > Angel Pieiro.
> > > 
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> > 
> > -- 
> > David van der Spoel, Ph.D.
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> > 
> > 
> > ------------------------------
> > 
> > Message: 4
> > Date: Tue, 29 Jan 2008 19:26:06 +0100
> > From: Ran Friedman <r.friedman at bioc.uzh.ch>
> > Subject: Re: [gmx-users] torsion potential with 7 parameters
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <479F6FBE.6040207 at bioc.uzh.ch>
> > Content-Type: text/plain; charset=UTF-8
> > 
> > David van der Spoel wrote:
> > >
> > > in the worst case you can add two dihedrals, however n = 6,7 is not
> > > implemented. you can however tabulate this if I'm not mistaken.
> > Isn't the bonded tabulated paramers due only in GMX 4.0?
> > Ran.
>