[gmx-users] is there any tool for flexibility?

João M. Damas jmdamas at itqb.unl.pt
Sun Sep 1 18:53:37 CEST 2013

trjorder might be of some help to deal with the exchange events.


On Sun, Sep 1, 2013 at 5:28 PM, Albert <mailmd2011 at gmail.com> wrote:

> On 09/01/2013 06:03 PM, Justin Lemkul wrote:
>> Maybe g_msd or g_rmsf, but I don't think there's anything specifically
>> designed to address water molecules, and the term "flexibility" can have
>> far too many meanings ;)
>> -Justin
> thanks a lot for kind messages.
> but there are a lot of water molecules in those region. Moreover, those
> water molecules can exchange with bulk environment. In this case, it would
> be very difficult to use g_msd or g_rmsf for this purpose.....
> I don't know which tool or which method would be good to describe this
> observation...
> --
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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