VMD-L Mailing List
From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Tue Feb 02 2016 - 01:34:46 CST
- Next message: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Previous message: Monika Madhavi: "Re: Updating atomselections in every frame and write to a pdb"
- Next in thread: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Reply: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
- Next message: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Previous message: Monika Madhavi: "Re: Updating atomselections in every frame and write to a pdb"
- Next in thread: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Reply: Axel Kohlmeyer: "Re: What is the correct way of using "pbcwrap" with "atomselect [within]"?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]