Tom wrote: > If you read this part of the manual again you will see that it discusses > this point of 1-4 interactions for the OPLS forcefield and RB dihedrals > (and the same as discussed for OPLS is true for the AMBER forcefields using > RB potentials for dihedrals). > > Tom >
Thanks very much for your comment, and excuse me for my late reply. I guess this method may not work, although the function form has been transformed to normal dihedral function, the calculated dihedral energy still includes 1-4 vdw(during the function transformation, calculated energy doesn't change). So in this case(when the dihedral paremeters are deduced from RB parameters), even we are using normal dihedral function(V=A(1+cos(nw+w0)), we still need to exclude 1-4 vdw. In fact, in GMX manual page 102, I found that 1-4 vdw is deduced from normal vdw, by multiplying a scaling factor(this scaling scheme is utilized by amber FF, but GMX force field doesn't treat 1-4 vdw by scaling), so I have changed this scaling factor of 1-4 vdw to 0.0, and found 1-4 vdw energy became 0 in the energy minimization output. This is how I exclude 1-4 vdw now, but I have not found any other users who posted that they have solved this problem in the same way, so I think I need to consult the mailing list further whether this solve is right or wrong. Yang Xunjie 2009-12-2 > --On Friday, November 20, 2009 16:45:44 +0800 XunJie Yang > <yangx...@mail.ustc.edu.cn> wrote: > > > Hello GMX users: > > I'm new to GMX and I'm now facing a problem. For short, it is about how > > to properly use the RB function. I'm now doing simulation with AMBER > > force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans > > function for dihedral, it is how FFAmber forcefield treats dihedral > > angles as the parameters provided are only for RB function. According > > to GMX Manual page 62, using RB function implies exclusion of 1-4 LJ > > interactions between the first and last atom of the dihedral, which > > means, I should turn off the 1-4 vdw term while retaining the 1-4 coulomb > > term. However, I haven't found the way of doing so. If I deleted the > > [pairs] block in the topology file, all 1-4 interactions including 1-4 > > coulomb interaction would be deleted. Could anyone who knows key to > > this problem give me some help? Thanks in advance! > > > > Yang Xunjie > > 2009-11-20 > > -- -- 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
