GROMACS version: 2021.2
GROMACS modification:
Dear GROMACS users,
I am trying to simulate ice growth in presence of hBN nanosheet and ice layer in the simulation box. I use the CHARMM36m force field.
I have the coordinates for ice atoms modelled with TIP4P in the PDB file. The residue name for ice is “ICE” and I have 636 residue for ice. The ice layer is chain A. I should also mention that there will be position restraint with force constant of 1000 kJ mol−1 nm−1 on the ice molecules.
I added this residue name in residuetypes.dat file, defined this residue with its atoms and bonds in merged.rtp file as below:
[ ICE ] ; From tip4p.itp file and ffnonbonded.itp
[ atoms ]
OW OWT4 0.000 0
HW1 HWT4 0.520 0
HW2 HWT4 0.520 0
MW MWT4 -1.04 0
[ bonds ]
OW HW1
OW HW2
And I added the parameters for bond and angle in bonded parameters file in the force field as below:
[bondtypes]
OWT4 HWT4 1 0.09572000 502416.00 ; From tip4p.itp file
[angletypes]
HWT4 OWT4 HWT4 5 104.520000 628.020000 0.00000000 0.00 ; From tip4p.itp file
Also I have the below parameters in non-bonded parameters file:
#ifdef HEAVY_H
OWT4 8 9.951400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O
HWT4 1 4.032000 0.52 A 0.0 0.0 ; TIP4p H
MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP 4p vsite
#else
OWT4 8 15.999400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O
HWT4 1 1.008000 0.52 A 0.0 0.0 ; TIP4p H
MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP4p vsite
#endif
I was able to generate the topology, create the simulation box and solvate the system but in the next command line which is:
“gmx grompp -f em.mdp -c solvate.gro -r solvate.gro -p init.top -o solvate.tpr -maxwarn 1”
the system complains about the mass of the dummy atom and I got errors for each residue of ice as follows:
“ERROR 1 [file init.top, line 52]:
atom MW (Res TIP4-30) has mass 0 (state A) / 0 (state B)”
I need to generate separate posre.itp file for ice so that I can restrain ice residues.
I would appreciate if someone could help me to solve this problem.