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Department of Chemistry and Chemical Biology |
Questions and problems?Energy minimizationDoes the parameter NSNB (number of steps between two updates of the nonbonded list) influence the energy gradient? For me it looks as if the energy gradient is reset. If I set NSNB equal to MAXCYC (Maximum number of cycles) the minimization is successful, but if I keep NSNB to the default value of 25 the minimizations ends up in an endless loop with no futher progress in the rms value of the energy gradient.Every time the nonbonded list is updated, the set of interacting atom pairs is likely to change, which can set the minimization off in a different 'direction'. It is even logically possible that a circular path could occur in this case, such that minimization would never terminate, although it is far more likely that the molecule would wander around indefinitely in a more-or-less infinitesmal space. One approach would be to set a step limit on the minimization - 100-500 is usually sufficient to prepare for running MD. Another solution (especially appropriate for fine-grain minimization for normal mode calculation) would be to set the cutoff to include the entire system and NSNB=9999999. Bill Ross Web Masters <webadmin@www.amber.ucsf.edu> Last modified: Mon Sep 18 12:57:16 PDT 1995 |
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