Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file.
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi all >> >> Do atoms belonging to the same charge group have to be indexed >> consecutively in the topology file or can you have the following. >> >> [atoms] >> 1 CA 1 CGE CA 1 -0.1150 12.0110 >> 2 CB 1 CGE CB 1 0.0000 12.0110 >> 3 CA 1 CGE CA 2 -0.1150 12.0110 >> 4 CB 1 CGE :wq >> CB 2 0.0000 12.0110 > > Assuming you fix this, then yes, splitting charge groups can work. > Use grompp -pp to see the post-processed topology to make sure > everything came out as expected. > > -Justin > >> 5 CA 1 CGE CA 3 -0.1150 12.0110 >> 6 CB 1 CGE CB 3 0.0000 12.0110 >> 7 HC 1 CGE HC 1 0.1150 1.0080 >> 8 CU 1 CGE CU 13 0.2650 13.0190 >> 9 NU 1 CGE NU 13 -0.5970 14.0070 >> 10 HC 1 CGE HC 2 0.1150 1.0080 >> 11 CU 1 CGE CU 14 0.2650 13.0190 >> 12 NU 1 CGE NU 14 -0.5970 14.0070 >> 13 HC 1 CGE HC 3 0.1150 1.0080 >> >> Cheers >> >> Gavin > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists