Hi
I have a martini system of 1642 atoms. Most of them are overlapping. I tried running energy minimization with all sorts of parameter manipulation but system doesn't resolve and crashes. I am wondering if GROMACS provide soft potential function like LAMMPS to relax system before running real MD simulation. or there is any other way of removing overlaps?
Kindly help.
energy minimization Script I am using:
integrator = steep
dt = 0.010
nsteps = 100000
cutoff-scheme = Verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb_switch = 0.0
rcoulomb = 1.1
epsilon_r = 15
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
You can start a new simulation starting from the old one’s endpoint.
Take your ending configuration (trjconv -dump to get a frame at the end of your .trr/.xtc, or use the final .gro file if your simulation completed), modify it to the new configuration. If you’re just changing the box size, gmx editconf works, though changing the box without adding/removing particles will likely lead to instability. If yo’re trying to do something like duplicate your box with all the components in extra dimensions, gmx genconf will work. Then (if atom counts have changed), update your topology/index file, and create a new tpr using those inputs, and go through all the normal equilibration steps.
Whether that’s worth all the effort vs restarting from scratch depends on how long your simulation ran and what you’re trying to do
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