> Hello, > > I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, > the periodic parameters of dihedral angles have been converted into > Ryckaert-Bellemans ones. I have tried to find more info about this in the > CHARMM and Gromacs documentations but I have not found much. Why exactly > this conversion should be done since the periodic potential is implemented > in both force fields? My problem is that several dihedral angles cannot be > easily converted in RB parameters since their multiplicities is equal to 6 > and the RB potential implemetation is limited to 5 constants.
To quote my own code comment, "# We need some elaborate functionality to convert the CHARMM dihedral type # of k * (1 + cos(n * xi - delta ) ) functions summed over n into something # GROMACS can implement. While the above functional form exists in # GROMACS, you can't have more than one function of this type, and # CHARMM has a number of dihedral interactions that require more than # one such function. However for delta = 0 or pi and n <= 5, then the above # cosine function can be expanded in powers of cos xi, and the coefficients # of the expansion can be summed in this conversion and presented to # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this # works because CHARMM only uses such delta and n values for atom type # combinations that need multiple functions of the above form. Warnings # are issued when delta is some other value, and the algorithm dies if # n is > 6. In order to simplify GROMACS logfile output so that it only # has to report one sort of dihedral term for most simulations, all # dihedral terms with n <= 5 are expressed as R-B, even when not necessary. # Dihedrals with n=6 are left in periodic form, since it is not possible # to convert these to R-B form when the summation is limited to the # fifth power of cos xi." So if you have a single dihedral over a set of atoms that has n>=6 then you can leave it in periodic form and the only cost is that you have to remember that the output will likely have both periodic and R-B dihedrals. If you have one such a dihedral in combination with others n<6 then you can use a combination of periodic and R-B. If you have multiple dihedrals with n>=6 you will need to hack the source code, except in some trivial cases, perhaps. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
