VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Tue Feb 02 2016 - 01:34:46 CST

Dear all,

I make my atom selections as follows
set sel [atomselect $mol "within 5 of index $ind1" frame $frm]

and I am taking similar selections for series of $ind1 s. However it seems
that all these selections does not have nearly same number of atoms which
should be since my system is isotropic. Then I think I have to wrap the
selections for the $ind1 s that might be at the edges of the box. But when
I used pbcwarp as follows, it says that it cannot make the atomselection
(is that because within 5 doesn't work because of wrapping?).

package require pbctools
set sel [atomselect $mol "within 5 of index $ind1" frame $frm]
pbc wrap -sel $sel1 -first $frm -last $frm

Any clarification regarding this is greatly appreciated.

Best regards,
Monika 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.