VMD-L Mailing List
From: Ondrej Kroutil (okroutil_at_gmail.com)
Date: Wed Nov 12 2014 - 17:52:22 CST
Dear VMD users,
I have a question about gofr routine.
I need to calculate gofr separately for solvent molecules above and below
plane of my planar molecule (which is centered in the box). So I got a
normal vector to this plane, assigned its components to variables a1 b1 and
set normal [ veccross [vecsub $v2 $v1] [vecsub $v3 $v1] ]
set a1 [lindex $normal 0]
set b1 [lindex $normal 1]
set c1 [lindex $normal 2]
and did selection of these solvent molecules using:
set up [atomselect 0 "name OW and $a1*(x-6.76)+$b1*(y-6.76)+$c1*(z-6.76)>
# set down [atomselect 0 "name OW and
Then I used "measure gofr" to get gofr:
set gr0 [measure gofr $pt $up delta 0.05 rmax 6.76 usepbc 1 selupdate 1
first 0 last -1 step 1]
But it seem to me than this set up uses for $up variables $a1 $b1 and $c1
just from the first frame and then just updates selection with these
So my question is if there is a way how to compute gofr when I need to
update variables in a selection?
Thank you very much.
-- Ondřej Kroutil ,, Faculty of Health and Social Studies ----"))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okroutil_at_gmail.com >------ O Mobile: +420 736 537 190