VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 02 2019 - 09:26:45 CDT

Hello Anupama, assuming that you are able to write a small Tcl loop for
this, you can either check "Update Selection every Frame" in the
representation menu or use the "*update*" sub-command of an atom selection:

set water [atomselect top "water and (not hydrogen) and (within 5.0 of
protein)"]
for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
    $water frame $i
    $water update
    .... Your analysis here
}
$water delete

On Wed, Oct 2, 2019 at 9:20 AM anupama sharma <anusharma.jan1995_at_gmail.com>
wrote:

> dear all,
> I want to extract the trajectory of water molecules near the protein
> surface within 5 angstorm region. I was able to do that in vmd but it is
> for only one time frame and than the water molecules diffuses away for the
> next time frame. I want to extract the trajectory of only those water
> molecules that are near protein surface within 5 angstorm region for each
> individual time frame so that i can get the complete trajectory of water
> molecules that are near the protein surface excluding the water molecules
> that diffuses away in each next frame......
> I will be thankful for help.
>
>
>
>
>
> Thanks and regards
> Anupama,
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin