hello GMX users: I am now using GMX together with FFamber, I found that the parameter files provided by FFamber uses RB functions (described in GMX manual p62) rather than normal dihedral function to calculate dihedral energy term. According to the manual(p62), when using RB function for dihedral angle, we should exclude 1-4 vdw interactions because this interaction has been included in the RB calculation. I have searched the FFamber homepage and found no comments or FAQ items about how to exclude 1-4 vdw and had to depend on myself, finally I found that, by changing the FudgeLJ variable in ffamber99.itp (the FF include file similar to ffgmx.itp) to 0.0, I successfully turn off the 1-4 vdw(as the 1-4 vdw energy in the EM result was zero). I am not much confident at what I did because the default value for FudgeLJ is 0.5 and is not 0.0, I just wonder why FFamber doesn't set FudgeLJ to 0.0, is it that they ignored this point? There must be many others using FFamber, so I want to know that, how do you solve this problem? Did you solve it the same way? Thanks for your help!
Yang Xunjie 2009-12-2 -- 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
