As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3).
[atoms] ; atomnr type resnr residue name cgnr charge mass 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 CB 2 0.0000 12.0110 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 14 CU 1 CGE CU 15 0.2650 13.0190 15 NU 1 CGE NU 15 -0.5970 14.0070 cgs: nr=112 cgs[0]={0..1} cgs[1]={2..3} cgs[2]={4..5} cgs[3]={6..6} cgs[4]={7..8} cgs[5]={9..9} cgs[6]={10..11} cgs[7]={12..12} cgs[8]={13..14} cgs[9]={15..16} cgs[10]={17..18} cgs[11]={19..20} cgs[12]={21..21} cgs[13]={22..23} cgs[14]={24..24} cgs[15]={25..26} cgs[16]={27..27} cgs[17]={28..29} cgs[18]={30..31} cgs[19]={32..33} cgs[20]={34..35} cgs[21]={36..36} cgs[22]={37..38} cgs[23]={39..39} cgs[24]={40..41} cgs[25]={42..42} cgs[26]={43..44} cgs[27]={45..46} Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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. >> > > Can you provide a relevant snippet of the gmxdump output to > demonstrate this? > > Consecutive numbering is not stated as a requirement in the manual, > and if it is in the code, then it needs to be either documented as > being necessary, and/or an enhancement request needs to be filed on > redmine for non-consecutive charge group numbering. > > -Justin > >> 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