CYANA Macro: anneal - Revision history

Miki: /* Description */

2010-01-12T13:41:11Z

Description

← Older revision		Revision as of 15:41, 12 January 2010
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	== Description ==		== Description ==

	Performs simulated annealing on the current structure with a total of N MD ''steps'', starting with Nhigh MD steps at temperature ''thigh'' followed by slow cooling during N - Nhigh MD steps to a final temperature of ''Tend''. Finally, n steps of conjugate gradient minimization are added. The temperature is measured in target function units per degree of freedom. Optionally, more minimization can be performed in order to relax strong overlaps and restraint violations prior to the start of the MD calculation. The '''relax''' option can be useful for larger (above 200 residues) proteins if otherwise the maximal length of the pair list would be exceeded.		Performs simulated annealing on the current structure with a total of N MD steps, starting with Nhigh MD steps at temperature ''thigh'' followed by slow cooling during N - Nhigh MD steps to a final temperature of ''Tend''. Finally, n steps of conjugate gradient minimization are added. The temperature is measured in target function units per degree of freedom. Optionally, more minimization can be performed in order to relax strong overlaps and restraint violations prior to the start of the MD calculation. The '''relax''' option can be useful for larger (above 200 residues) proteins if otherwise the maximal length of the pair list would be exceeded.

Miki at 13:38, 12 January 2010

2010-01-12T13:38:34Z

← Older revision		Revision as of 15:38, 12 January 2010
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	== Description ==		== Description ==

	Performs simulated annealing on the current structure with ~~the given~~ total of ~~torsion angle dynamics~~ ''steps'', starting with ~~''highsteps'' of torsion angle dynamics~~ at temperature ''thigh'' followed by slow cooling during ~~the remaining torsion angle dynamics~~ steps to a final temperature of ''~~tend~~''. Finally, ~~''minsteps''~~ of conjugate gradient minimization are ~~performed~~. The temperature is measured in target function units per degree of freedom. ~~More~~ minimization can be performed ~~with the '''~~relax~~''' option to reduce~~ strong overlaps and restraint violations prior to the start of the MD calculation. The '''relax''' option can be useful for proteins ~~with more than 250 residues to avoid excessively large target function values at~~ the ~~outset~~ of the ~~simulated annealing torsion angle dynamics~~.		Performs simulated annealing on the current structure with a total of N MD ''steps'', starting with Nhigh MD steps at temperature ''thigh'' followed by slow cooling during N - Nhigh MD steps to a final temperature of ''Tend''. Finally, n steps of conjugate gradient minimization are added. The temperature is measured in target function units per degree of freedom. Optionally, more minimization can be performed in order to relax strong overlaps and restraint violations prior to the start of the MD calculation. The '''relax''' option can be useful for larger (above 200 residues) proteins if otherwise the maximal length of the pair list would be exceeded.

Admin: /* Description */

2009-08-06T09:07:03Z

Description

← Older revision		Revision as of 11:07, 6 August 2009
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	== Description ==		== Description ==

	Performs simulated annealing on the current structure with a total of ~~N MD~~		Performs simulated annealing on the current structure with the given total of torsion angle dynamics ''steps'', starting with ''highsteps'' of torsion angle dynamics at temperature ''thigh'' followed by slow cooling during the remaining torsion angle dynamics steps to a final temperature of ''tend''. Finally, ''minsteps'' of conjugate gradient minimization are performed. The temperature is measured in target function units per degree of freedom. More minimization can be performed with the '''relax''' option to reduce strong overlaps and restraint violations prior to the start of the MD calculation. The '''relax''' option can be useful for proteins with more than 250 residues to avoid excessively large target function values at the outset of the simulated annealing torsion angle dynamics.
	steps, starting with ~~Nhigh MD steps~~ at temperature ~~Thigh~~ followed by slow
	cooling during ~~N - Nhigh MD~~ steps to a final temperature of ~~<math>T_{end}</math>~~. Finally,
	~~n steps~~ of conjugate gradient minimization are ~~added~~. The temperature is
	measured in target function units per degree of freedom. ~~Optionally, more~~
	minimization can be performed ~~in order~~ to ~~relax~~ strong overlaps and
	restraint violations prior to the start of the MD calculation. The relax
	option can be useful for ~~larger (above 200~~ residues~~) proteins if otherwise~~
	the ~~maximal length~~ of the ~~pair list would be exceeded~~.

Admin: /* Description */

2009-01-29T11:32:26Z

Description

← Older revision		Revision as of 13:32, 29 January 2009
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	Performs simulated annealing on the current structure with a total of N MD		Performs simulated annealing on the current structure with a total of N MD
	steps, starting with Nhigh MD steps at temperature Thigh followed by slow		steps, starting with Nhigh MD steps at temperature Thigh followed by slow
	cooling during N - Nhigh MD steps to a final temperature of <math>~~T_end~~</math>. Finally,		cooling during N - Nhigh MD steps to a final temperature of <math>T_{end}</math>. Finally,
	n steps of conjugate gradient minimization are added. The temperature is		n steps of conjugate gradient minimization are added. The temperature is
	measured in target function units per degree of freedom. Optionally, more		measured in target function units per degree of freedom. Optionally, more

Admin: /* Description */

2009-01-29T11:31:44Z

Description

← Older revision		Revision as of 13:31, 29 January 2009
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	Performs simulated annealing on the current structure with a total of N MD		Performs simulated annealing on the current structure with a total of N MD
	steps, starting with Nhigh MD steps at temperature Thigh followed by slow		steps, starting with Nhigh MD steps at temperature Thigh followed by slow
	cooling during N - Nhigh MD steps to a final temperature of ~~Tend~~. Finally,		cooling during N - Nhigh MD steps to a final temperature of <math>T_end</math>. Finally,
	n steps of conjugate gradient minimization are added. The temperature is		n steps of conjugate gradient minimization are added. The temperature is
	measured in target function units per degree of freedom. Optionally, more		measured in target function units per degree of freedom. Optionally, more

Admin at 11:31, 29 January 2009

2009-01-29T11:31:03Z

← Older revision		Revision as of 13:31, 29 January 2009
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	'' Simulated annealing''		''Simulated annealing''

	== Parameters ==		== Parameters ==

Admin at 11:30, 29 January 2009

2009-01-29T11:30:44Z

← Older revision		Revision as of 13:30, 29 January 2009
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			'' Simulated annealing''

	== Parameters ==		== Parameters ==

Admin: 1 revision

2009-01-29T11:26:58Z

1 revision

New page

== Parameters ==

; thigh=''real'': (default: 8.0)
; steps=''integer'': (default: 10000)
; highsteps=''integer'': (default: -1)
; minsteps=''integer'': (default: 1000)
; relax

== Description ==

Performs simulated annealing on the current structure with a total of N MD
steps, starting with Nhigh MD steps at temperature Thigh followed by slow
cooling during N - Nhigh MD steps to a final temperature of Tend. Finally,
n steps of conjugate gradient minimization are added. The temperature is
measured in target function units per degree of freedom. Optionally, more
minimization can be performed in order to relax strong overlaps and
restraint violations prior to the start of the MD calculation. The relax
option can be useful for larger (above 200 residues) proteins if otherwise
the maximal length of the pair list would be exceeded.