CYANA Macro: anneal: Difference between revisions
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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 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. | ||
steps, starting with Nhigh MD steps at temperature | |||
cooling during N - Nhigh MD steps to a final temperature of | |||
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.