VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Oct 02 2019 - 09:24:07 CDT

Hi Anupama,

You will need to update your selection in each frame. Something like this

set sel [atomselect top "...blah..."]

for < i-loop over frames > {

$sel frame $i
$sel update

..
}

Hope this helps,

Chitrak.

On Wed, Oct 2, 2019 at 6:58 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,
>
>