[gmx-users] Regarding minimum size
jalemkul at vt.edu
Mon Mar 12 19:17:32 CET 2018
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.
> 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
>> 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.
>> 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:
>>>> This is regarding the minimum size or resolution used in gromacs for
>>>> sampling coordinates of atoms. I know that the maximum size is the
>>>> 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
>>> image convention, but one could simulate even a few atoms in the gas
>>> if desired.
>>> 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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Justin A. Lemkul, Ph.D.
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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