GROMACS version:2025.2
GROMACS modification: No
When I use this mdp to neutralize the system I am getting some notes.
minim.mdp:
; ions.mdp - used as input into grompp to generate ions.tpr
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 50000
nstlist = 1 ;
cutoff-scheme = Verlet
ns_type = grid
coulombtype = cutoff
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz
Outputs:
Command line:
gmx grompp -f minim.mdp -o minim.tpr -c solv.gro -p topol.top -n index.ndx
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -281059331
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘POPG’
Excluding 3 bonded neighbours molecule type ‘DCLE’
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 25]:
System has non-zero total charge: -388.000000
Total charge should normally be an integer.
for discussion on how close it should be to an integer.
Number of degrees of freedom in T-Coupling group rest is 473517.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature
NOTE 3 [file minim.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
But it works.
Then I run energy minimization after this with this mdp:
integrator = steep
emtol = 1000.0
nsteps = 5000
nstlist = 10
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
constraints = h-bonds
constraint_algorithm = LINCS
Then I get some errors while running
gmx grompp -f ions.mdp -o neutral.tpr -c neutral.gro -p topol.top -n index.ndx
gmx mdrun -v -deffnm neutral
And these were in the results, although the system converged to the desired steepest descent.
step 18: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Step 34, time 0.034 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000066, max 0.010883 (between atoms 7281 and 7280)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
7282 7280 35.2 0.1110 0.1108 0.1111