https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_grid_search 2026-04-08T21:23:03Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Commands:_grid_search&diff=4560&oldid=prev 2009-01-28T23:35:41Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; tfcut=&#039;&#039;real&#039;&#039;: (default: 0.0)<br /> ; test <br /> <br /> == Description ==<br /> <br /> This command performs a grid search for the current fragment (as<br /> defined by the most recent &#039;&#039;&#039;grid fragment&#039;&#039;&#039; command). The grid search<br /> will be done over all torsion angles in the fragment and with the<br /> number of steps per torsion angle given by the variable &#039;&#039;&#039;nstep&#039;&#039;&#039;. If<br /> the cutoff value given by the &#039;&#039;&#039;tfcut&#039;&#039;&#039; for the local, fragment-based<br /> target function is positive, then all conformations with a local<br /> target function value below this cutoff will be considered as<br /> allowed. Otherwise, a conformation will be allowed if no single<br /> restraint violation exceeds the corresponding &quot;soft&quot; cutoff values<br /> defined by the variables soft_upl, soft_lol, soft_vdw, soft_aco, and<br /> soft_cco. Other types of restraints, e.g. residual dipolar couplings<br /> or pseudocontact shifts, cannot be used in grid searches.<br /> <br /> To avoid excessive computation times for fragments with many angles<br /> and/or few restraints, the calculation is not started if the expected<br /> number of grid points to be checked (after the evaluation of restraints<br /> that involve a single torsion angle) exceeds the value of the variable<br /> &#039;&#039;&#039;gridpoints&#039;&#039;&#039;. Similarly, a grid search is aborted if the estimated<br /> total computation time in seconds exceeds gridtime seconds. If the<br /> number of grid points to be checked (after evaluation of the restraints<br /> that depend on a single dihedral angle) is larger than Nmax, or if<br /> the estimated computation time for the complete grid search exceeds<br /> tmax seconds, the calculation will be stopped.<br /> <br /> If the &#039;&#039;&#039;test&#039;&#039;&#039; option is set, the grid search will not be started but<br /> the expected number of grid points to be checked (after evaluation<br /> of the restraints that depend on a single dihedral angle) will be<br /> reported.<br /> <br /> The grid search is restricted to angle values that are allowed<br /> according to the standard grid memory, A. The resulting allowed angle<br /> values from the grid search will again be stored in the standard<br /> grid memory.<br /> <br /> Further reading:<br /> <br /> Guntert et al. J. Biomol. NMR 12, 543-548 (1998). Guntert et<br /> al. J. Am. Chem. Soc. 111, 3997-4004 (1989).</div>

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