From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Nov 02 2011 - 00:06:35 CDT
At present you can't (as far as I know). However you can use the below
function to find the center of mass and perhaps select the atom closest to that
set of coordinates.
proc center_of_mass {selection} {
# some error checking
if {[$selection num] <= 0} {
error "center_of_mass: needs a selection with atoms"
}
# set the center of mass to 0
set com [veczero]
# set the total mass to 0
set mass 0
# [$selection get {x y z}] returns the coordinates {x y z}
# [$selection get {mass}] returns the masses
# so the following says "for each pair of {coordinates} and masses,
# do the computation ..."
foreach coord [$selection get {x y z}] m [$selection get mass] {
# sum of the masses
set mass [expr $mass + $m]
# sum up the product of mass and coordinate
set com [vecadd $com [vecscale $m $coord]]
}
# and scale by the inverse of the number of atoms
if {$mass == 0} {
error "center_of_mass: total mass is zero"
}
# The "1.0" can't be "1", since otherwise integer division is done
return [vecscale [expr 1.0/$mass] $com]
}
Best,
Chris
PS - please don't cross post on the mailing lists. Since the radial distribution tool is a VMD plugin, post to the vmd-l list. Thanks.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-0329 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 Swarna M Patra <swarnam.patra_at_gmail.com> writes: > Date: Wed, 2 Nov 2011 10:24:06 +0530 > From: Swarna M Patra <swarnam.patra_at_gmail.com> > To: vmd-l_at_ks.uiuc.edu, namd-l_at_ks.uiuc.edu > Subject: namd-l: selection of cholesterol molecules > > Dear NAMD/VMD users, > I am trying to calculate the radial distribution of cholesterol molecules > around a particular helix . For that I am using the Radial distribution > given in VMD. for the 1st selection I give "protein and resid 1 to 50" and > for 2nd selection I give "resname CHL1" that is cholesterol molecule. which > actually takes each atom of cholesterol and try to see if it is there or > not. How can I give the 2nd selection to take Center of mass of cholesterol > molecule not center of mass of each atom. > please give me some suggestions > thanks > swarna
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