Dear Gromacs Users, I have a question to create a topology file with tabulated potentials.
I have two molecules in coarse-grained beads. The first molecules are 5 beads and 3 types (A-B-C-B-A), and the second molecules are 3 beads and 2 types (D-E-D). A-B bond potential tabulated in table_b1.xvg B-C bond potential tabulated in table_b2.xvg D-E bond potential tabulated in table_b3.xvg A-B-A angle potential tabulated in table_a1.xvg B-C-B angle potential tabulated in table_a2.xvg D-E-D angle potential tabulated in table_a3.xvg I created topol.top file as follows. Can I seperate two section of [ atoms ] for two molecules? If it is ok, can I assign the number of the second molecule in [ atoms ] from 1 to 3 again? As you see, the first [ atoms ] section, the bead numbers are assigned from 1 to 5, and the second [ atoms ] section, the bead numbers are '*AGAIN*' assigned from 1 to 3. The simulation run fine but I am not sure this topology file is ok. Thank you very much. [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 0.0 0.0 [ atomtypes ] ;type mass charge ptype sigma epsilon A 75.087799 0.000 A 1.000000000 1.000000000 B 76.097998 0.000 A 1.000000000 1.000000000 C 42.080999 0.000 A 1.000000000 1.000000000 D 74.103099 0.000 A 1.000000000 1.000000000 E 100.161398 0.000 A 1.000000000 1.000000000 [ moleculetype ] ; Name nrexcl Other_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 A 1 RES A1 1 0.000000 75.087799 2 B 1 RES B1 2 0.000000 76.097998 3 C 1 RES C 3 0.000000 42.080999 4 B 1 RES B2 4 0.000000 76.097998 5 A 1 RES A2 5 0.000000 75.087799 [ bonds ] 1 2 8 1 1.0; 1:bond:1 2 3 8 2 1.0; 1:bond:2 3 4 8 2 1.0; 1:bond:3 4 5 8 1 1.0; 1:bond:4 [ angles ] 1 2 3 8 1 1.0; 1:angle:1 2 3 4 8 2 1.0; 1:angle:2 3 4 5 8 1 1.0; 1:angle:3 [ dihedrals ] 1 2 3 4 8 1 1.0; 1:dihedral:1 2 3 4 5 8 1 1.0; 1:dihedral:2 [ moleculetype ] ; Name nrexcl Other_chain_B 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 D 2 Other_chain_B D1 1 0.000000 74.103099 2 E 2 Other_chain_B E 2 0.000000 100.16139 3 D 2 Other_chain_B D2 3 0.000000 74.103099 [ bonds ] 1 2 8 3 1.0 ; 1:bond:1 2 3 8 3 1.0 ; 1:bond:2 [ angles ] 1 2 3 8 3 1.0 ; 1:angle:1 [ system ] ; Name Built with Packmol [ molecules ] ; Compound #mols Other_chain_A 200 Other_chain_B 100 Best regards, Changwoon Jang, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.