Hi I have a silly question about the implementation of the Gromos forcefield in gromacs, particularly about the exclusions. I have the gromos manual and have seen that, for instance, for the residue MET there are only 1st and 2nd neighbors exclusions defined for it. However, when I build a protein using the gromos forcefield in gromacs and print out the exclusions generated (using gmxdump), I get more than the ones I would get according to gromos.
I am trying to validate my results by comparing with someone else's run that was performed using gromos directly and the description of the molecules don't seem to match in that part. The file dumped from gromos has only the exclusions defined as in the gromos manual. I assume they should be equivalent and both codes should give rise to the same forcefield description but I would greatly appreciate if someone could comment on this so I can understand better how to compare these two files. Also, if someone knows how to transform gromacs truncated octahedral coordinates to a format that can be read by gromos I would really appreciate it. Thanks!! -- **************************************** Romelia Salomon Miller Group 132 Noyes Chemistry Department Caltech _______________________________________________ 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
