[gmx-users] Interaction across PBC

[Steven Neumann]

Thanks a lot

Steven


On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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