[gmx-users] Regarding minimum size

[Justin Lemkul]

On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote:
> I think the minimum coordinates are (0,0,0)
>

Not really. GROMACS will accept negative coordinates and then re-wrap 
them into the periodic box with its origin at (0,0,0).

An actual error message and full command from the OP would be helpful here.

-Justin

> 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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>

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================