CYANA Macro: anneal: Difference between revisions

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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.

Latest revision as of 14:41, 12 January 2010

Simulated annealing

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.

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