[gmx-users] Interaction across PBC

[Steven Neumann]

Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.

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


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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>