[gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

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.

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?

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.

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>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)
>>
>>  --
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-- 
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)
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