[gmx-users] Regarding minimum size

[Srinivasa Ramisetti]

I think the minimum coordinates are (0,0,0)

Srinivasa
On 12/03/2018 18:01, Chhavi Yadav wrote:
> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
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>>
>> ==================================================
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