VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 16 2020 - 09:02:07 CST

On Mon, Nov 16, 2020 at 9:28 AM SHRAVANI NETHI . <
p20160500_at_hyderabad.bits-pilani.ac.in> wrote:

> Thanks alot for the suggestion sir..
> I need it explicitly for my further analysis. I hope u suggested to do
> this with tcl scripting. I will try it out.
>

yes, but keep in mind that VMD assumes that the number of atoms and atom
identities do not change within a trajectory, so any further
post-processing or analysis within VMD will have to also process those
files one at a time.

> Shravani
> On Mon, 16 Nov, 2020, 7:12 PM Axel Kohlmeyer, <akohlmey_at_gmail.com> wrote:
>
>>
>>
>> On Mon, Nov 16, 2020 at 8:35 AM SHRAVANI NETHI . <
>> p20160500_at_hyderabad.bits-pilani.ac.in> wrote:
>>
>>> Dear vmd users,
>>> I have been trying to find the dynamics if water between clay layers.
>>> I selected the water between layers using "exwithin".
>>> The water molecules keep on changing between these layers during
>>> simulation.
>>> When i am trying to save the updated coordinates of these dynamic water
>>> molecules that does not remain same at each time frame into new pdb file
>>> using save coordinates in vmd, i found that the coordinates of only those
>>> water molecules selected at definite timeframe are being saved throughout
>>> trajectory.
>>>
>>> How can save coordinates of those water molecules that are present
>>> between layers with updation of trajectory i.e. the water molecules that
>>> are not fixed and keep on change between layers with trajectory updation??
>>>
>>
>> you have to do this in a loop writing out a single file for a single
>> frame and with updating the selection in between.
>> updating a selection is a costly operation and thus it is only done when
>> explicitly requested.
>>
>> axel.
>>
>>
>>
>>>
>>> Any suggestions will be highly appreciated.
>>> Thanks in advance
>>>
>>> Shravani
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.