[gmx-users] Gromacs 5.1 - trouble with insert-molecules

[Dan Gil]

Hi,

I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox,"
which I was able to use without a problem.

With gromacs 5.1, I am using insert-molecules to generate my initial
configuration containing water, ethanol, and a lennard-jones particle which
I defined. When I attempt to minimize the energy using "steep", the program
crashes, apparently due to clashes.

Even an initial configuration containing only ethanol atoms will crash as
well.

As an additional side note, I was able to run the program on a personal
computer using single-precision. When I run it with double-precision, it
crashes.

I think that perhaps I am not using insert-molecules correctly, so I will
show you the commands I used.

---
Preconditions: I begin with solute.gro file containing 1 atom. There is
ethanol.gro and water.gro which contains the coordinates of 1 molecules of
ethanol and water, respectively.

First I insert a number of ethanol molecules.
gmx insert-molecules -f solute.gro -ci ethanol.gro -box 6 6 6 -nmol
numberOfEthanols -o out.gro

Then I insert a number of water molecules.
gmx insert-molecules -f out.gro -ci water.gro -box 8 8 8 -nmol
numberOfWaters -o + out2.gro
---

Best Regards,

Dan