[gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Mark Abraham]

Hi,

Likely you're just generating clashes and sometimes getting lucky, e.g
because your vdW radii is guessed badly if you don't manage it.

Mark

On Wed, 15 Jun 2016 17:10 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.
>
> Here is an excerpt of the error right before the program crashes:
>
> Step 19, time 0.038 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms nan, max 0.005299 (between atoms 9321 and 9317)
>
> -----
>
> Also another 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.
>
> Best Regards,
>
> Dan
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