Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n >= 6 don't come alone. For exemple in Arg :
HD1 HE | | | // --CG--CD--NE--CZ | | \ HD2 is defined by 6 dihedral with n>=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ)> They are all of the same type (X-CT2-CT2-X). So, if I understand well, the result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are not a combination of different type of dihedrals with n >= 6. The problems happen when a combination of different types of dihedral are used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type B). In this case, one possibility is to hack the Gromacs code by allowing a 6th Ryckaert-Bellemans parameter (?) Cheers Nico >> 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 gmx-users@gromacs.org > 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 > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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