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.abra...@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@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-requ...@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)
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