[gmx-users] stopped simulation

[Justin Lemkul]

On 11/6/13 4:52 PM, Mark Abraham wrote:
> On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
>>
>>> Many thanks Justin. What is an appropriate cut-off value? My box size is
>>> d=
>>> 0.5 nm; based on the definition of cut-off radius, its value shouble be
>>> smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I
>>> right?
>>>
>>>
>> No.  The cutoff value is not a function of box size; it is a fixed
>> property of the force field.  No wonder the simulation is crashing.  If
>> your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting
>> interactions across PBC!
>>
>
> Triple counting is not possible, per minimum-image convention. I think

True.  Thinking too quickly ;)

> Ehsan's report of a "0.5nm" box size is probably wrong, e.g. per its
> documentation, editconf -d 0.5 does not produce a 0.5nm box.
>

editconf -box 0.5 does produce such a box, though, so it is possible.  grompp 
should have warned quite obviously about the combination of a 0.5-nm box with 
1.5-nm cutoffs, though.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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