[gmx-users] Three molecules in single topol.top file

[Chang Woon Jang]

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,