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Minimization

This is taken from the CHARMM Minimization Documentation
Another good source is this documentation on the Minimization Commands

What is it?

Removing non physical contacts/interactions that come from the original construction of the file. This is done by running a smaller simulation that prepares your file for your intended simulation.

Why minimize?

More accurate results and remove disturbances. Possible that simulation will error out if not minimized correctly.

What algorithm options are there?

Two very common methods - Steepest Descent (SD) and Adopted Basis Newton Method (ABNR). CONJugate-gradient method and the POWEll minimizer are other methods that may be appropriate for special cases. Lesser used methods include Newton-Raphson minimization (NRAP) and Truncated-Newton (TN) minimization (TNPACK).

Steepest Descent (SD)

About: Simplest algorithm that moves coordinates in negative direction of the gradient. The ‘step size’ is the only adjustable parameter, which determines how much the coordinates are shifted at each step. Quickly improves the conformation when the GRMS is high (i.e. when the system is far from a minimum). Does not generally converge to a local minimum.

When/how to use: Use SD for the initial 25-50 steps (or longer) of minimization to remove bad contacts. Afterwards switch to ABNR to finish off the minimization.

Adopted Basis Newton Method (ABNR)

Will recognize when the structure is minimized and will auto exit, there is no danger in running ABNR for too long. TOLGradient command can be added to tell the minimizer to exit once a specified GRMS is achieved. TOLEnergy command can be added to tell the minimizer to exit once the change in energy is less than the specified amount.

When/how to use: After running SD switch to ABNR to finish off the minimization.

How do I know if it is minimized?

It is considered minimized when the root mean squared deviation of the gradient (GRMS) is very close to zero.

Minimization Process

Step 1) Load up PSF and coordinate file set into CHARMM

Step 2) Perform minimization

Step 3) Write out minimized coordinate file

Example