CHARMM c36b1 dimens.doc

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                          How to set CHARMM to run with any size system

        There are two ways to change the run-time size of charmm
arrays to accomodate a system of any size: from command line, and from
the charmm input (input file or standard input). Currently only the
maximum number of atoms can be set, and other sizes like maximum
number of residues, bonds, angles, segments, and so on, are set by an
approximation based on number of atoms specified.

Command line:

$ charmm -chsize nnnnnnnn

where nnnnnnnn is the maximum number of atoms in your system, for instance 200000.

Input file:

Use the charmm command dimension (only dime needs to be specified) immediately after the title:
* title
*
dimension chsize 200000