[gmx-users] Re: gmx-users Digest, Vol 45, Issue 120

[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.