Hello.
I am using Maritini CG FF on Gromacs 5.1.4. I am doing a system were I have:
PolarWater box | Benzene box | Polarwater box
I have a protein at both interfaces.
The steps I follow for my simulation after I create the box are: 1) EM, 2) short NVT for equilibration (POSRE for the protein), 3) short NPT for equilibration (POSRE for the protein), and finally a long MD (NVT with no POSRE). All part of the simulation are run at pressure of 1 bar and temperature of 298K.
My initial gro file for the benzene is:
3
1BENZ R1 1 0.420 0.536 0.370
1BENZ R2 2 0.425 0.288 0.263
1BENZ R3 3 0.238 0.352 0.448
0.72300 0.78400 0.72100
Then I just use:
gmx genconf -f benzene_dens_box.gro -o benzene_solvated.gro -nbox 21 19 19
gmx editconf -f benzene_solvated.gro -o benzene_box.gro -box 12.5 12.5 14
Where the benzene_box.gro is box I insert in the middle of the two PolarWater boxes to create the interfaces.
When I do the box for the Benzene, I achieve a very similar density compared to the real density (876kg/m3).
But when I do the NPT, my density increases to 1200kg/m3.
The main parameters of my mdp file for the NPT part of my simulation is:
define = -DPORES
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
vdw_type = cutoff
vdw-modifier = Potential-shift-Verlet
rvdw = 1.2
coulombtype = Reaction-field
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.2
epsilon_r = 2.5 ; for polarizable water
epsilon_rf = 0
tcoupl = v-rescale
tc-grps = system
tau_t = 1
ref_t = 298
Pcoupl = berendsen
Pcoupltype = isotropic
;nstpcouple = -1 ; default value of -1 sets nsttcouple equal to nstlist
tau_p = 3.0
compressibility = 4.5e-5
ref_p = 1.0
Please help me to achieve with some guidance so that my density keeps relatively the same initial density before the NPT run.
I must be doing something wrong.
The beads are the one already given by the martini itp file for solvents, so the mistake must be around my mdp file I guess.
Thanks.
It seems you are using position restrained in NPT simulation. Just remove the line define = -DPOSRES. Then it has to be Ok.
Thanks,
But the position restrained is only for the protein and not the benzene. Therefore the POSRE should not affect my benzene density right?
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