[gmx-users] Interaction across PBC

[Justin Lemkul]

On 4/23/13 9:15 AM, Steven Neumann wrote:
> Shall I specify one index group for two regions or 2 seprate? g_mindist
> asks just for one group.
>

If it only takes one, then you can only give it one.

> would twice as cutoff would be sufficent to assess they do not interact?
>

Probably, maybe less, but that depends on the cutoff itself.  Water ordering can 
persist for up to 2.0 nm or so.

-Justin

>
> On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>> Thank you.
>>
>> Steven
>>
>>
>> On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 4/23/13 6:37 AM, Steven Neumann wrote:
>>>
>>>> Dear Gmx users,
>>>>
>>>>
>>>> My protien has got some strong acidic and strong basic parts. I fold and
>>>> unfold my protein with different temperaturss. I bserved high affinity of
>>>> those regions towards each other, they are very close to each other over
>>>> the simulation.
>>>>
>>>> How can I possibly check whether my two regions do not interact across
>>>> the
>>>> boundary conditions with such high affinity?
>>>>
>>>>
>>> g_mindist -pi with a suitable index group.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================**==========
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
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>>
>>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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