[gmx-users] gmx insert-molecules

[Dave Michael]

Hi guys,

I've got a system of 400 water molecules (
http://md.chem.rug.nl/index.php/example-applications2/solvent-systems) and
I want to make and simulate a system with 1k, 10k, 100k and 1M particles.

So far, I've done:
gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
-radius 0.05
(what I've tried doing is double the box volume and double the number of
particles and it didn't work without -radius 0.05 / default radius doesn't
add new molecules to the system)
And I got a file with 800 particles, some of them have negative coordinates
(I presume those are initial coordinates) and no initial velocities.

Running (GROMACS 5.1.2) md on that file doesn't work as the simulation
hangs @ step 0. Using gmx energy I can see that the total energy and
temperature are off the scales but the density is fine (990 kg/m^3)

I don't have much experience in the chemical / physical aspects, can you
please tell me (step by step if possible) what I missed and what should I
do next?

Dave