Dear Gromacs Users, I have a single topol.top file containing three molecules. Does this format is correct because the simulation keeps failing?
Thank you. [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 0.0 0.0 [ atomtypes ] ;type mass charge ptype sigma epsilon A 59.088399 0.000 A 1.000000000 1.000000000 B 194.236395 0.000 A 1.000000000 1.000000000 C 74.103099 0.000 A 1.000000000 1.000000000 D 99.153398 0.000 A 1.000000000 1.000000000 E 88.106799 0.000 A 1.000000000 1.000000000 F 74.079799 0.000 A 1.000000000 1.000000000 [ moleculetype ] TDM 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 A 1 TDM A1 1 0.000000 59.088399 2 A 1 TDM A2 2 0.000000 59.088399 3 B 1 TDM B1 3 0.000000 194.236395 4 A 1 TDM A3 4 0.000000 59.088399 5 A 1 TDM A4 5 0.000000 59.088399 [ bonds ] 1 3 8 1 1.0 ; 1:bond:1 2 3 8 1 1.0 ; 1:bond:2 3 4 8 1 1.0 ; 1:bond:3 3 5 8 1 1.0 ; 1:bond:4 [ angles ] 1 3 2 8 1 1.0 ; 1:angle:1 1 3 4 8 1 1.0 ; 1:angle:2 1 3 5 8 1 1.0 ; 1:angle:3 2 3 4 8 1 1.0 ; 1:angle:4 2 3 5 8 1 1.0 ; 1:angle:5 4 3 5 8 1 1.0 ; 1:angle:6 [ moleculetype ] J230 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 C 1 J230 C1 1 0.000000 74.103099 2 D 1 J230 D1 2 0.000000 99.153398 3 C 1 J230 C2 3 0.000000 74.103099 [ bonds ] 1 2 8 2 1.0 ; 1:bond:1 2 3 8 2 1.0; 1:bond:2 [ angles ] 1 2 3 8 2 1.0 ; 1:angle:1 [ moleculetype ] JMT 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 C 1 JMT C3 1 0.000000 74.103099 2 D 1 JMT D2 2 0.000000 100.161398 3 E 1 JMT E1 3 0.000000 88.106799 4 E 1 JMT E2 4 0.000000 88.106799 5 E 1 JMT E3 5 0.000000 88.106799 6 E 1 JMT E4 6 0.000000 88.106799 7 E 1 JMT E5 7 0.000000 88.106799 8 E 1 JMT E6 8 0.000000 88.106799 9 E 1 JMT E7 9 0.000000 88.106799 10 E 1 JMT E8 10 0.000000 88.106799 11 E 1 JMT E9 11 0.000000 88.106799 12 F 1 JMT F1 12 0.000000 74.079799 [ bonds ] 1 2 8 2 1.0 ; 1:bond:1 2 3 8 3 1.0 ; 1:bond:2 3 4 8 4 1.0 ; 1:bond:3 4 5 8 4 1.0 ; 1:bond:4 5 6 8 4 1.0 ; 1:bond:5 6 7 8 4 1.0 ; 1:bond:6 7 8 8 4 1.0 ; 1:bond:7 8 9 8 4 1.0 ; 1:bond:8 9 10 8 4 1.0 ; 1:bond:9 10 11 8 4 1.0 ; 1:bond:10 11 12 8 5 1.0 ; 1:bond:11 [ angles ] 1 2 3 8 3 1.0 ; 1:angle:1 2 3 4 8 4 1.0 ; 1:angle:2 3 4 5 8 5 1.0 ; 1:angle:3 4 5 6 8 5 1.0 ; 1:angle:4 5 6 7 8 5 1.0 ; 1:angle:5 6 7 8 8 5 1.0 ; 1:angle:6 7 8 9 8 5 1.0 ; 1:angle:7 8 9 10 8 5 1.0 ; 1:angle:8 9 10 11 8 5 1.0 ; 1:angle:9 10 11 12 8 6 1.0 ; 1:angle:10 [ dihedrals ] 1 2 3 4 8 1 1.0 ; 1:dihedral:1 2 3 4 5 8 2 1.0 ; 1:dihedral:2 3 4 5 6 8 3 1.0 ; 1:dihedral:3 4 5 6 7 8 3 1.0 ; 1:dihedral:4 5 6 7 8 8 3 1.0 ; 1:dihedral:5 6 7 8 9 8 3 1.0 ; 1:dihedral:6 7 8 9 10 8 3 1.0 ; 1:dihedral:7 8 9 10 11 8 3 1.0 ; 1:dihedral:8 9 10 11 12 8 4 1.0 ; 1:dihedral:9 [ system ] ; Name Built with Packmol [ molecules ] ; Compound #mols TDM 106 J230 100 JMT 12 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.