[gmx-users] two molecules in a single topology file

[Chang Woon Jang]

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,