Dear colleagues, I'm looking for clarifications on what exactly I need to do in order to get a correct scaling of 1-4 interactions for OPLS-AA in a topology made by x2top. Specifically, will the command
x2top -f in.gro -o out.top result in a topology that, when fed into grompp, will give a .tpr that is correct in this respect? Or should I use the same command with the -nopairs option and let grompp generate the pairs basing on the [ defaults ] section of ffoplsaa.itp? Or did I miss the correct way to use x2top altogether (nexcl=4? something with dihedrals? etc.)? I'm trying to check if OPLS parameters are suitable for the description of a somewhat unusual system, and so far, the geometry of the system seems to get distorted by some intramolecular nonbonded interactions; I'd like to know whether that's because of unsuitable FF parameters, a bad topology, or both :) The version of GROMACS is presently 3.3.3, but I'm actually going to use 4.x. for this once I know how to use x2top properly. Thanks in advance, Vasilii
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
