Re: [Jmol-users] minimize constraints in a script

[Robert H. <ha...@st...>]

*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 <GWh...@nc...>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