Re: how to quantify and visualize the flow of water into a protein

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Jul 08 2014 - 19:12:40 CDT

Στις 9 Ιουλ 2014 3:04 ΠΜ, ο χρήστης "Thomas Evangelidis" <tevang3_at_gmail.com>
έγραψε:
>
> Hi
>
> I thought about water density too, but it doesn't give you much
information about water influx. Water is always present at the entrance
points but gets in and out spontaneously.

I meant sporadically.

>
> Στις 9 Ιουλ 2014 2:40 ΠΜ, ο χρήστης "Maxim Belkin" <mbelkin_at_ks.uiuc.edu>
έγραψε:
>
>> Hi Thomas,
>>
>> This question is not really related to NAMD. A better place for
'analysis' type of questions is VMD mailing list.
>>
>> Anyway, If your trajectory fits into RAM, you can use VMD volmap plugin
to compute water density distribution averaged across the entire
simulation. However, manual scripting might be required if "entry points"
move around.
>>
>> Maxim
>>
>>
>> On Jul 8, 2014, at 6:20 PM, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
>>
>>> Greetings,
>>>
>>> Is anyone aware of any tool that helps visualize and/or quantify the
flow of water into a transporter from an MD trajectory? I have a long
trajectory of a transporter and want to find the main entrance points of
water. I can see by manual inspection the various entrance points but it is
difficult to decide which is/are the most important.
>>>
>>> thanks,
>>> Thomas
>>>
>>> --
>>>
>>> ======================================================================
>>>
>>> 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/
>>>
>>>
>>

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