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

[Thomas Evangelidis]

Why not calculate the hydration map?


On 1 September 2013 19:29, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/13 12:28 PM, Albert 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.....
>>
>>
> Well, you wouldn't analyze everything at once, that's what index groups
> are for.
>
>
> -Justin
>
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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/