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

[João M. Damas]

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

Best,
João


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
Tel:+351-214469613