Questions and problems?

Energy minimization

Does 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

My goal is to find a very low gradient accurately on a large system without allowing the system to collapse on itself due to the large number of steps required using conjugate gradient methods. I have run the structure thru 600 steps of steepest descent followed by 1000 steps of conjugate gradient all the while keeping the backbone atoms completely constrained. After releasing the backbones I ran an additional 1000 steps of conjugate gradient. This results in a structure that has not collapsed very much but has a reasonable amount of relaxation from the initial hand built conformation.

Dave Case
usig nmode ... minimizing from the initial hand built conformation

You are using a minimizer designed to grind small molecules to the absolute lowest energies for a huge, hand-built model. This is like trying to clean Brooklyn Bridge with a toothbrush. To make such a model reasonable, it is way way better in my experience to run md in the range of 1-100K, possibly using belly or restraints to keep structure in the parts you trust more.

Bill Ross