CYANA Command: 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 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. | ||
Latest revision as of 14:36, 5 August 2009
Parameters
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.