[gmx-users] Interaction across PBC
s.neumann08 at gmail.com
Tue Apr 23 15:15:23 CEST 2013
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.
> 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
>>> boundary conditions with such high affinity?
>> g_mindist -pi with a suitable index group.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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