Thank you for the information
Fernando
On Tue, 10 Apr 2012 07:58:51 -0400, David A Case wrote:
> On Tue, Apr 10, 2012, Fernando Martín García wrote:
>>
>> We are performing a long MD and we have observe a perturbation in
>> one
>> residue that have been stable during the whole simulation, until it
>> has
>> reached the limit of the water box (we are using PBC isotropic
>> conditions) and we are asking if the change of the conformation
>> could
>> have been provoked by a pressure change in the limit of the box.
>
> No: under periodic boundary conditions, there is no "limit" to the
> box, and
> the edge of the box is no different than the middle, etc. For
> example, you
> could use the "center" and "image" commands in ptraj to make it look
> like
> any part of your molecule is at the very center of the box.
>
> ....dac
>
>
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--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 5.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
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Received on Tue Apr 10 2012 - 05:30:04 PDT
