VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Thu May 25 2017 - 02:13:12 CDT

Hello to all

I am trying to remove sudden RMSD jumps between two segments (AP1 and AP2),
observed as an artefact of periodic conditions.

I have tried the commands below (or similar variations), but have not been
able to resolve this:

pbc unwrap -sel "segname AP1 AP2"

pbc wrap -all -sel "segname AP1 AP2" -compound fragment -compoundref
"segname AP1 AP2" -center unitcell -centersel "segname AP1"

I think this should be working as per the PBCTools manual:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Please let me know if there is any error or some omission in the commands.
Feel free to ask for further information. 

-- 
Cheers
Peter