[gmx-users] Regarding minimum size

[Chhavi Yadav]

Hi Justin,
Thanks for the reply.

I meant this : In our application, we need to randomly sample coordinates
for atoms. When we were doing that, we got an error message for one of the
random coordinate samples because the sample coordinate was smaller than
the minimum coordinates. What is this minimum coordinate and how can I find
its value?

I hope the question is clear now.

Thanks,
Chhavi

On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/12/18 1:30 PM, Chhavi Yadav wrote:
>
>> Hello,
>>
>> This is regarding the minimum size or resolution used in gromacs for
>> sampling coordinates of atoms. I know that the maximum size is the matrix
>> box. Can someone please let me know what the minimum is?
>>
>
> I'm not sure if this is the answer to your question, but GROMACS can
> perform MD for any number of particles. The minimum box size depends on the
> cutoff values required for a given force field, as required by the minimum
> image convention, but one could simulate even a few atoms in the gas phase
> if desired.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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