From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Tue Jul 08 2014 - 19:43:35 CDT
Hi Thomas,
If your trajectory is very large, reading in that in VMD might take a lot
of memory, which might cause your tcl to crash to run very slowly, you
might resort to CHARMM for analysis. You can calculate RMSD and
autocorrelation functions easily with CHARMM.
Hope it helps.
-Mo
On Tue, Jul 8, 2014 at 5:20 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> That's true. You can write your own tcl script to analyze water flux:
> simply track displacements of water oxygens.
>
>
> On Jul 8, 2014, at 7:04 PM, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
>
> 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. This is not captured by water
> density.
> 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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