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
c1:

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)>
0"]
# set down [atomselect 0 "name OW and
$a1*(x-6.76)+$b1*(y-6.76)+$c1*(z-6.76)<0"]

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
coefficients.
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.

    Ondrej Kroutil 

-- 
Ondřej Kroutil
        ,,              Faculty of Health and Social Studies
   ----"))'             University of South Bohemia
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