GROMACS version:2021.6
GROMACS modification: No
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Dear Gromacs users
I have the same problem as in
How to treat specific water molecules as ligand?.
I’m setting .top file for MD simulation with OPC model for water.
I want to use positional constraints on the three waters(name: FIX) that coordinate to the sodium ion.
Using the above link’s answer, I have rewritten the [settles] section.
Are there any other sections to be rewritten?
[ moleculetype ]
; Name nrexcl
FIX 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 FIX rtp FIX q 0.0
1 OW 1 FIX O 1 0.00000000 16.000000 ; qtot 0.000000
2 HW 1 FIX H1 2 0.67914200 1.008000 ; qtot 0.679142
3 HW 1 FIX H2 3 0.67914200 1.008000 ; qtot 1.358284
4 EP 1 FIX EPW 4 -1.35828400 0.000000 ; qtot 0.000000
#ifdef FLEXIBLE
[ bonds ]
; ai aj funct c0 c1 c2 c3
2 1 1 0.08724 462750.400000
3 2 1 0.13712 462750.400000
3 1 1 0.08724 462750.400000
#else
[ constraints ]
1 2 1 0.08724331
1 3 1 0.08724331
2 3 1 0.13712051
#endif
[ virtual_sites3 ]
; Site from funct
4 1 2 3 1 0.147721 0.147721
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
#ifdef REST_ON
#include "/home/itp/posre_FIX.itp"
#endif