VMD-L Mailing List

From: Luis Agullo (luis.agullo_at_lagullo.com)
Date: Fri Sep 12 2014 - 12:29:04 CDT

Thanks a lot! I have tried:

> pbc wrap -all -centersel "segid P1" -center com -compound fragment

Really, it seems that 'fragment' functions much better than 'segment'
(although in my system I think both should be identical). Many frames
are now perfectly aligned. Unfortunately, in some frames monomers remain
separated. I am now trying with "pbc join fragment' after the wrap
function...

Luis