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

[David van der Spoel]

Ángel Piñeiro wrote:
> 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? 
It could well be that you'll have to wait for 4.0 for the tabulated 
dihedrals.

You can however specify two torsion potentials around the same bond. 
This is how it is done routinely in CHARMM, where there are even more 
than two for some torsions.

> 
> 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.
> 
> 
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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