VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Oct 02 2019 - 09:43:30 CDT

Hi Anupama,

You can't write out a trajectory for this kind of selection, because the number of atoms changes from frame to frame, which breaks typical trajectory formats, as well as some assumptions VMD makes internally. If there was some core set of water molecules that doesn't change, or if you wanted to pick the 100 closest water molecules, some clever tcl scripting can do what you want. Would that be helpful?

-Josh

On 2019-10-02 07:59:44-06:00 owner-vmd-l_at_ks.uiuc.edu 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,