[gmx-users] converting parmbsc0 dihedrals to RB function

[Mark Abraham]

On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:
> Dear Dr. Mark,
>
> Thanks very much for pointing out that GROMACS can handle multiple
> instances of the parameters with different n for a single dihedral.

I hope I'm right there. There's been discussion on such topics before. 
There's some subtle difference between [ dihedrals ] and [ dihedraltypes 
] which eludes my memory, but which will be in the archives.

> However, given that, in the existing ffamber ports in GROMACS  the other
> dihedral parameters have been converted to RB form, would it make a
> difference to just import these new parameters in the non-RB form?

It will make no numerical difference, but g_energy will probably report 
the contribution from the two different functional forms separately. 
Attempting to mix *non-bonded* interactions in this kind of way asks for 
trouble, because the maths is not well-defined. Here, you're fine, 
because the maths is right.

> To my knowledge, the torsional term should not vary (or, vary within
> acceptable limits) irrespective of the functional form used to calculate
> it. But I would like to know if there could be some reason for which
> this assumption cannot be made.

The R-B form might be more efficient to evaluate than a sum of simple 
dihedrals in the cases where the angle is zero or 180, which might 
explain the ffamber practice.

Mark

> Dear Dr. Alan,
>
> Thanks very much for pointing out to the acpypi code. I was able to
> better understand the conversion procedure.
>
> Sincerely,
> Vignesh
>
> On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>
>         Dear Users,
>
>         I am trying to port the new parmbsc0 forcefield
>         (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
>         simulations.
>
>         While unit conversions are sufficient to convert many of the
>         parameters
>         from AMBER to GROMACS format, dihedral angle conversion does not
>         seem to
>         be straight forward - the dihedral parameters need to be
>         converted to
>         the Ryckaert-Bellemans parameters.
>
>
>     Why? GROMACS can probably do the non-RB form - IIRC you can
>     implement a sum of multiple instances of 4.61 with different n.
>
>
>         I went through the GROMACS 4.0
>         manual, especially equations 4.61-4.65 to understand the
>         procedure. The
>         procedure involves comparing the fourier expansion of the IUPAC
>         convention of dihedral potential (equation 4.65) with the
>         Ryckaert-Bellemans (RB) functional of dihedral potential
>         (equation 4.62)
>         to get the Cn's of the RB function. However, I am not able to
>         understand
>         how to account for the phase angles. (Also to note, the parmbsc0
>         forcefield contains phase angles other than 0 and 180.)
>
>
>     Elegant conversion formulae require those angles to be convenient...
>
>     Mark
>
>
>           Any advice or suggestion will be of great help.
>
>         Thank you,
>
>         Vignesh
>
>         --
>         R.Vigneshwar
>         Graduate Student,
>         Dept. of Chemical & Biomolecular Engg,
>         National University of Singapore,
>         Singapore
>
>         "Strive for Excellence, Never be satisfied with the second Best!!"
>
>         I arise in the morning torn between a desire to improve the
>         world and a
>         desire to enjoy the world. This makes it hard to plan the day.
>         (E.B. White)
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> R.Vigneshwar
> Graduate Student,
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> Singapore
>
> "Strive for Excellence, Never be satisfied with the second Best!!"
>
> I arise in the morning torn between a desire to improve the world and a
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>