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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] torsion potential with 7 parameters
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
------------------------------
Message: 4
Date: Tue, 29 Jan 2008 19:26:06 +0100
From: Ran Friedman <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] torsion potential with 7 parameters
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
