VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jun 11 2015 - 12:24:23 CDT

Hello:

Following the splitting of a homotetramer into intact trimer/monomer at ca
300 ns trajectory, I tried the following three commands in the tk console
of the remote visualization for the last 24h simulation (ca 11 GB file
size). I had 64GB memory available (the max I could have)

set all [atomselect top all]

pbc unwrap -sel all (which operated very slowly on the 4999 frames)

pbc wrap -sel all

The latter created a box of lines of the original size. Then, command "all
not water" removed those pertaining to water, leaving lines not amenable
to any "Drawing Method". These lines looked like long bonds, which were
not present in the splitted system.

I used "all" as the system is also composed of ligands, some firmly
residing into binding pockets, some other ones traveling from the
surrounding medium to their binding pockets.

The "intact" in the first line above is not entirely correct. That is, the
monomer is removed from the homotetramer without its major ligand (the
substrate to be modified by the enzyme).

Thanks for suggestions about how to amend my faulty commands.

francesco pietra