FEP calculations in Gromacs
Free energy of hydration of NMA
ITP file for NMA
[ moleculetype ]
; name nrexcl
NMA 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 opls_235 1 NMA C 1 0.50
2 opls_236 1 NMA O 1 -0.50
3 opls_238 1 NMA N 1 -0.50
4 opls_135 1 NMA CT 1 -0.18
5 opls_242 1 NMA CT 1 0.02
6 opls_241 1 NMA H 1 0.30
7 opls_140 1 NMA HC 1 0.06
8 opls_140 1 NMA HC 1 0.06
9 opls_140 1 NMA HC 1 0.06
10 opls_140 1 NMA HC 1 0.06
11 opls_140 1 NMA HC 1 0.06
12 opls_140 1 NMA HC 1 0.06
[ bonds ]
1 2 1
1 3 1
1 4 1
3 5 1
3 6 1
5 7 1
5 8 1
5 9 1
4 10 1
4 11 1
4 12 1
[ pairs ]
; i j funct
1 7
1 8
1 9
2 5
2 6
2 7
2 8
2 9
2 10
2 11
2 12
3 10
3 11
3 12
4 5
4 6
4 7
4 8
4 9
5 10
5 11
5 12
6 7
6 8
6 9
6 10
6 11
6 12
7 10
7 11
7 12
8 10
8 11
8 12
9 10
9 11
9 12
[ angles ]
2 1 3 1
2 1 4 1
1 3 5 1
1 3 6 1
3 5 7 1
3 5 8 1
3 5 9 1
1 4 10 1
1 4 11 1
1 4 12 1
3 1 4 1
5 3 6 1
10 4 11 1
10 4 12 1
11 4 12 1
7 5 8 1
7 5 9 1
8 5 9 1
[ dihedrals ]
5 3 1 2 3
6 3 1 5 3
7 5 3 1 3
10 4 1 2 3
11 4 1 10 3
12 4 1 10 3
6 3 1 2 3
5 3 1 4 3
6 3 1 4 3
11 4 1 2 3
12 4 1 2 3
10 4 1 3 3
11 4 1 3 3
12 4 1 3 3
8 5 3 1 3
9 5 3 1 3
7 5 3 6 3
8 5 3 6 3
9 5 3 6 3
Create a topol.top file for just NMA
#include "ffoplsaa.itp"
#include "nma.itp"
[ system ]
; name
OPLSAA NMA in water
[ molecules ]
; name number
NMA 1
For generating cubic water box with a size of approximately 3 nm
> editconf -f nma.gro -o nma_box.gro -c -d 1.5 -bt cubic
> genbox -cp nma_box.gro -cs spc216.gro -o nma_water_box.gro -p topol.top