VMD-L Mailing List

From: SHRAVANI NETHI . (p20160500_at_hyderabad.bits-pilani.ac.in)
Date: Mon Nov 16 2020 - 08:04:04 CST

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.

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.
>