GROMACS version: 2021.4
GROMACS modification: Yes/No
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Hello everyone!!
Hope you’re having a nice day!
I have a question regarding the workflow of GROMACS when using PACKMOL to create a solvent box. Since im going to use organic solvents in the near future im setting up a baseline condition in water for comparisons. So instead of using the gmx solvate cmd i made everything on packmol. Now given the fact that i have a net charge of 3 im trying to neutralize my system (since i dont want to take the risk of getting artifacts) im using the following cmds:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
problem is im getting this after the gmx grompp cmd:
Fatal error:
Box was shifted at least 10 times.
I tried to increase the box dimensions in the .gro file but to no avail.
Below is my ions.mdp file:
; LINES STARTING WITH ‘;’ ARE COMMENTS
title = Minimization ; Title of run
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = cutoff ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
My complex is a protein (pH 4) and ligand (at pH4 too) previously treated in charm-gui and cgenff respectivelly.
I will be very thankful for your help :) !