Optimising a path - Revision history

import>Mp466 at 20:13, 12 May 2010

2010-05-12T20:13:40Z

← Older revision		Revision as of 20:13, 12 May 2010
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	rate constant as far as possible, by keeping track of the rate constants as function of the		rate constant as far as possible, by keeping track of the rate constants as function of the
	number of minima in the databases. Eventually additions of new connections to the database		number of minima in the databases. Eventually additions of new connections to the database
	will no longer reduce the rate constant.		will no longer reduce the rate constant. Focus on the DIJKSTRA 0 path, both its length, and
			the MFPT that it estimates.

	The primary keywords to use when improving the rate constants are SHORTCUT, SHORTCUT BARRIER, and		The primary keywords to use when improving the rate constants are SHORTCUT, SHORTCUT BARRIER, and
	FREEPAIRS. Aggressive shortcutting of either variety may be required, but one should be careful		FREEPAIRS. Aggressive shortcutting of either variety may be required, but one should be careful
	about it introducing artificial traps, which can be alleviated with FREEPAIRS.		about it introducing artificial traps, which can be alleviated with FREEPAIRS.
			For the FREEPAIRS calculations, focus on the NGT rate constants.


	Some bits of data should be tracked when performing this calculation.		Some bits of data should be tracked when performing this calculation.

import>Em427 at 15:59, 1 October 2008

2008-10-01T15:59:36Z

← Older revision		Revision as of 15:59, 1 October 2008
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	Some bits of data should be tracked when performing this calculation.		Some bits of data should be tracked when performing this calculation.

	0. Check what's going on structurally in the highest-barrier processes: examine the corresponding sections of the path; maybe look at a movie (of those transitions... ;-). OPTIM keywords CHECKCHIRALITY and NOCISTRANS (for CHARMM ~~only?~~) should be used to stop unphysical isomerizations getting into the database in the first place.		0. Check what's going on structurally in the highest-barrier processes: examine the corresponding sections of the path; maybe look at a movie (of those transitions... ;-). OPTIM keywords CHECKCHIRALITY and NOCISTRANS (for both CHARMM and AMBER) should be used to stop unphysical isomerizations getting into the database in the first place.

	1. Periodically make a disconnectivity graph from the database (with or without grouping as necessary)		1. Periodically make a disconnectivity graph from the database (with or without grouping as necessary)

import>Jmc49 at 09:18, 23 September 2008

2008-09-23T09:18:39Z

← Older revision		Revision as of 09:18, 23 September 2008
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	connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha		connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha
	is a too low (i.e too negative) of a MAXTSENERGY value can make an apparent connection disappear! The aim is to		is a too low (i.e too negative) of a MAXTSENERGY value can make an apparent connection disappear! The aim is to
	grow the database until one sees a plateau in the GT (grouped) rate constant as a function of		grow the database until one sees a plateau in the GT (probably grouped) rate constant as a function of
	number of local minima. A plateau of around an order of magnitude is usually accurate enough.		number of local minima. A plateau of around an order of magnitude is usually accurate enough.

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	about it introducing artificial traps, which can be alleviated with FREEPAIRS.		about it introducing artificial traps, which can be alleviated with FREEPAIRS.

	~~Three~~ bits of data should be tracked when performing this calculation.		Some bits of data should be tracked when performing this calculation.

			0. Check what's going on structurally in the highest-barrier processes: examine the corresponding sections of the path; maybe look at a movie (of those transitions... ;-). OPTIM keywords CHECKCHIRALITY and NOCISTRANS (for CHARMM only?) should be used to stop unphysical isomerizations getting into the database in the first place.
⚫	1. ~~Also periodically~~ make a disconnectivity graph from the database (with or without grouping as necessary)

		⚫	1. Periodically make a disconnectivity graph from the database (with or without grouping as necessary)
	to check for introduced traps.		to check for introduced traps.

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	rates of the existing database.		rates of the existing database.

	3. Check the GT rate every n cycles with a "GT 0 <n>" line. Might be useful if n is chosen to be large (as a possibly expensive GT calculation on a large database every cycle is not good...) Otherwise check the rate with a separate pathsample job e.g. when you're making a tree.		3. Check the GT rate constant every n cycles with a "GT 0 <n>" line. Might be useful if n is chosen to be large (as a possibly expensive GT calculation on a large database every cycle is not good...) Otherwise check the rate with a separate pathsample job e.g. when you're making a tree.

import>Jmc49 at 17:32, 22 September 2008

2008-09-22T17:32:39Z

← Older revision		Revision as of 17:32, 22 September 2008
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	rates of the existing database.		rates of the existing database.

	3. Check the GT rate every n cycles with a "GT 0 <n>" line. Might be useful if n is chosen to be large; ~~otherwise~~ check the rate with a separate pathsample job e.g. when you're making a tree.		3. Check the GT rate every n cycles with a "GT 0 <n>" line. Might be useful if n is chosen to be large (as a possibly expensive GT calculation on a large database every cycle is not good...) Otherwise check the rate with a separate pathsample job e.g. when you're making a tree.

import>Jmc49 at 17:26, 22 September 2008

2008-09-22T17:26:25Z

← Older revision		Revision as of 17:26, 22 September 2008
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	Once a connection has been thought to be made, it is best to verify that there is indeed a		Once a connection has been thought to be made, it is best to verify that there is indeed a
	connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha		connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha
	is a too ~~high~~ of a MAXTSENERGY value can make an apparent connection disappear! The aim is to		is a too low (i.e too negative) of a MAXTSENERGY value can make an apparent connection disappear! The aim is to
	grow the database until one sees a plateau in the GT (grouped) rate constant as a function of		grow the database until one sees a plateau in the GT (grouped) rate constant as a function of
	number of local minima. A plateau of around an order of magnitude is usually accurate enough.		number of local minima. A plateau of around an order of magnitude is usually accurate enough.

import>Mp466 at 23:18, 19 September 2008

2008-09-19T23:18:04Z

import>Mp466 at 23:12, 19 September 2008

2008-09-19T23:12:42Z

@@ Line 3: / Line 3: @@
 Once a full connection has been thought to be made, it is best to verify that there is indeed a
 connection.  Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0.  A common gotcha
-is a too high of a MAXTSENERGY value can make an apparent connection disappear!
+is a too high of a MAXTSENERGY value can make an apparent connection disappear!  The aim is to
 The next goal is to optimise the mean first passage time, by building a larger database
@@ Line 16: / Line 18: @@
 number of minima in the databases.  Eventually additions of new connections to the database
 will no longer reduce the rate constant.

import>Mp466 at 22:56, 19 September 2008

2008-09-19T22:56:36Z

New page

Under construction...

Once a full connection has been thought to be made, it is best to verify that there is indeed a
connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha
is a too high of a MAXTSENERGY value can make an apparent connection disappear!

The next goal is to optimise the mean first passage time, by building a larger database
that has more direct connections between the starting and ending minima. In pathdata,
COMMENT DIJINITCONTFLY 0 and add SHORTCUT <n>, where n is perhaps a quarter of the
path length, or less if the path is huge. Using DUMMYRUN in pathdata can help in
setting the value for <n> because a list of pairs to connect will be created etc.
but no actual OPTIM jobs will be submitted. Setting too large or too small <n>
will be inefficient with respect to improving the rate constants. To begin with one
rate constant is likely to be much smaller than the other one. You want to optimise the
rate constant as far as possible, by keeping track of the rate constants as function of the
number of minima in the databases. Eventually additions of new connections to the database
will no longer reduce the rate constant.

← Older revision		Revision as of 23:18, 19 September 2008
Line 1:		Line 1:
	Under construction...		Under construction...

	Once a ~~full~~ connection has been thought to be made, it is best to verify that there is indeed a		Once a connection has been thought to be made, it is best to verify that there is indeed a
	connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha		connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha
	is a too high of a MAXTSENERGY value can make an apparent connection disappear! The aim is to		is a too high of a MAXTSENERGY value can make an apparent connection disappear! The aim is to
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	number of local minima. A plateau of around an order of magnitude is usually accurate enough.		number of local minima. A plateau of around an order of magnitude is usually accurate enough.

	The ~~next~~ goal is to optimise the mean first passage time, by building a larger database		The goal is to optimise the mean first passage time, by building a larger database
	that has more direct connections between the starting and ending minima. In pathdata,		that has more direct connections between the starting and ending minima. In pathdata,
	COMMENT DIJINITCONTFLY 0 and add SHORTCUT <n>, where n is perhaps a quarter of the		COMMENT DIJINITCONTFLY 0 and add SHORTCUT <n>, where n is perhaps a quarter of the
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	The primary keywords to use when improving the rate constants are SHORTCUT, SHORTCUT BARRIER, and		The primary keywords to use when improving the rate constants are SHORTCUT, SHORTCUT BARRIER, and
	FREEPAIRS. Aggressive shortcutting of either variety may be required, but one should be careful		FREEPAIRS. Aggressive shortcutting of either variety may be required, but one should be careful
	about it introducing ~~atrificial~~ traps, which can be alleviated with FREEPAIRS.		about it introducing artificial traps, which can be alleviated with FREEPAIRS.

	Three bits of data should be tracked when performing this calculation.		Three bits of data should be tracked when performing this calculation.

	1. Also periodically make a ~~tree~~ from the database (with or without grouping as necessary) ~~to check for~~		1. Also periodically make a disconnectivity graph from the database (with or without grouping as necessary)
	introduced traps.		to check for introduced traps.

	2. The pathsample output lines starting with Dijkstra> will provide the most information about the		2. The pathsample output lines starting with Dijkstra> will provide the most information about the
	rates of the existing database.		rates of the existing database.