Perfect, thanks.
We're having some fun, now.
George
________________________________
From: Robert Hanson [[email protected]]
Sent: Wednesday, December 18, 2013 10:15 PM
To: [email protected]
Subject: Re: [Jmol-users] minimize constraints in a script
Generally the minimization runs in its own thread. If it is desired to wait
until the process has completed prior to continuing, use set
useMinimizationThread false.
So I'm guessing that without that the rotation command halts the ongoing
minimization before you notice anything.
On Wed, Dec 18, 2013 at 7:19 PM, Whitwell, George
<[email protected]<mailto:[email protected]>> wrote:
Greetings,
I'm trying to explore rotational steric hindrance with partial success. From
the console, this series of commands:
minimize constraint {C5} {C3} {C1} {H6} 60 // or whatever angle is
indicated
minimize
minimize energy
work as advertised. I can:
rotate branch {C3} {C1} 60 60
and repeat the minimization at a new torsion angle. Of course, I want to use
the power of Jmol script to automate the investigation. When I run these lines:
zap; load SYNC "file:///C:/Compchem/s-pentane/spentane.xyz"
rotdeg = 120
var steps=360/rotdeg
measure delete
measure {C5}{C3}{C1}{H6}
for (var i=0;i<steps;i++) {
rotate branch {C3} {C1} @rotdeg 60
conang = getproperty("measurementinfo[1].value")
print conang
script inline ("minimize constraint {C5} {C3} {C1} {H6} @conang")
minimize Steps 500
minimize
show minimization
minimize energy }
either as:
script "C:\Compchem\s-pentane\rotation.spt"
or by pasting into the console, I get rotations, but no minimization. It
prints the angle, reports the Initial MMFF and the "show minimization" report
has a section for contraints, although none are specified:
C O N S T R A I N T S
---------------------
---------------------
Not a wiggle do I get from the molecule as it breezes around the circle. Any
ideas out there?
Thanks,
George Whitwell
NCWC - Chemistry
For the sake of completeness, "spentane.xyz" is pasted here:
17
C 0.00679 0.03015 0.00260
C 0.92788 0.92359 0.83193
C -0.84948 -0.88283 0.88567
C -0.88496 0.87921 -0.90110
C -0.04442 -1.81120 1.79096
H 0.63109 -0.60981 -0.63251
H 1.47915 1.61518 0.19195
H 1.65692 0.34451 1.39972
H 0.34164 1.51743 1.53978
H -1.54380 0.25498 -1.50830
H -0.29104 1.50114 -1.57356
H -1.51253 1.54194 -0.29849
H -1.49875 -1.48148 0.23976
H -1.51200 -0.25707 1.49472
H 0.49906 -1.25500 2.55575
H 0.68519 -2.38126 1.21053
H -0.69411 -2.52260 2.30225
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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