Adk44: Created page with "When you're optimising a path using ''SHORTCUT'' and ''SHORTCUT BARRIER'', you often add many minima to the database, some of which will not be well connected. These minima ma..."

2019-05-13T09:17:34Z

Created page with "When you're optimising a path using ''SHORTCUT'' and ''SHORTCUT BARRIER'', you often add many minima to the database, some of which will not be well connected. These minima ma..."

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When you're optimising a path using ''SHORTCUT'' and ''SHORTCUT BARRIER'', you often add many minima to the database, some of which will not be well connected. These minima may be of low energy, but with a high barrier connecting them to the rest of the tree. Such minima act as kinetic traps and as such, can severely affect the rate calculated using PATHSAMPLE.

Some of these traps may be real, but a lot will not, and the high barrier is simply the result of a lack of sampling. The ''UNTRAP'' keyword is designed to focus [[PATHSAMPLE]] reconnections on these minima, and hopefully find lower energy pathways to reconnect them to the rest of the database.

== Fine tuning parameters for UNTRAP ==

When using ''UNTRAP'', you can use more than the minimal arguements. From the [http://www-wales.ch.cam.ac.uk/PATHSAMPLE.2.1.doc/node5.html documentation]:

<pre>
UNTRAP einc thresh edeltamin elowbar
</pre>

Only the first two arguments are required (einc and thresh). However, you may find that ''UNTRAP'' is not picking pairs of minima efficiently. You can tweak the algorithm using the last two arguments recently implemented by Vanessa.

===edeltamin===
The optional arguments edeltamin and elowbar are useful for databases without a well-defined global minimum. If the potential energy difference between the minimum in question and the lowest product minimum is less than edeltamin, the value of edeltamin is substituted for this difference. This substitution prevents connection attempts to minima connected by low barriers but with a very small energy difference to the lowest product minimum.

===elowbar===
If the barrier from the minimum in question to the lowest product minimum is less than elowbar, a value of TINY(1.0D0) is given to the barrier instead. This substitution prevents connection attempts to minima connected by low barriers.

== Choosing values by visualising the effect==

Unless you have a very small database, the only way to check that your changes to ''UNTRAP'' are achieving what you're aiming for is to label the pairs of minima being selected by [[PATHSAMPLE]] on a disconnectivity graph. You can use the visualise_UNTRAP.sh script to do this. It can be found in the svn repository here:

<pre>
SCRIPTS/PATHSAMPLE/visualise_UNTRAP.sh
</pre>

The workflow for calibrating these values is as follows:

# Choose initial values by examining the disconnectivity graph for your system.
# Run [[PATHSAMPLE]] using the ''DUMMYRUN'' keyword, and kill it as soon as you see 'getupair> connecting minima' in the output.
# Run the ''visualise_UNTRAP.sh'' script, specifying the [[PATHSAMPLE]] output file, and the number of pairs of minima you'd like to label.
# Run ''disconnectionDPS'' to generate a disconnectivity graph.
# Visualise it using ''gv'' to see if ''UNTRAP'' is choosing the right minima.
# If it is, remove ''DUMMYRUN'' and submit the real job. Otherwise play with the values of ''edeltamin'' and ''elowbar'' and repeat.

The ''visualise_UNTRAP.sh'' script simply adds ''IDMIN'' lines to your existing ''dinfo'' for each minimum being connected.

[[Image:UNTRAPexample.png|thumb|Disconnectivity graph with pairs of minima highlighted|200px|right]]

This was produced using CHARMM19 with the following ''pathdata'' file:

<pre>
EXEC /home/csw34/svn/OPTIM/bin/pgi/COPTIM
TEMPERATURE 0.592
CHARMM
NATOMS 147
ITOL 1.0D0
GEOMDIFFTOL 0.1
EDIFFTOL 1.0D-6
PERMDIST
DIRECTION AB
COPYFILES perm.allow input.crd
PLANCK 9.536D-14

DUMMYRUN
SSH
CPUS 1
CYCLES 100
UNTRAP 2.0 65.0 1.0D-6 10.0
</pre>

Fine tuning UNTRAP - Revision history

Adk44: Created page with "When you're optimising a path using ''SHORTCUT'' and ''SHORTCUT BARRIER'', you often add many minima to the database, some of which will not be well connected. These minima ma..."