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

[Mark Abraham]

Hi,

I think I answered this a week ago.

Mark

On Fri, Jun 17, 2016 at 4:05 PM Dan Gil <dgilgmx at gmail.com> wrote:

> 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
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