MacroModel Reference Manual - ISP

Chapter 4: Operation CodesIn the context of MC or MC(JBW) simulations this command sets the number of degrees offreedom to be changed at each MC step or randomized at each MC(JBW) step. A degree offreedom is either a bond length, bond angle or torsion or a molecular translation or rotationalong or about a single axis. This number should be set in such a way to provide a compromisebetween acceptance rate and conformational interconversions. When args 1 and 2 of thiscommand differ, MCNV defines a range for the number of degrees of freedom to be changed ateach step. When the two arguments are identical, MCNV defines an exact number for the degreesof freedom to be changed at each step. In both cases, the initial values will be modified duringthe run by the adaptive mechanism unless debug 103 is defined.For MC, MC(JBW) or MCSD simulations, a number of degrees of freedom must be defined andconsequently, the MCNV command should be present; however, its two arguments can be 0, inwhich case the program will provide a default range, from 1 to maximum number of thedegrees of freedom of the molecules. Such a range is probably not efficient. For MC(JBW)/SD,no randomization in the JBW part is needed and all the randomization can effectively be doneby the SD part of the simulation. Doing so will increase the number of conformational interconversions.In order to achieve that, the MCNV command should be omitted and arg 2 of theMCSD command should be set to a negative number.arg1Minimum number of degrees of freedom altered0 Default: 1arg2Maximum number of degrees of freedom changed in a MC step0 Default: number of variable degrees of freedom in the system.arg4Cluster torsions varied at one timeThis is no longer seen as a useful option.0 Do not cluster torsions; recommended.1 All torsions rotated will be in a contiguous group as defined by the ordering of torsionsin the TORS commands.2 Allow a single intervening unused torsion.nIf, at a given stage, m torsions are rotated, these are selected from a contiguousgroup of (m+n–1) torsions selected from the list taken from the TORS commands.110MacroModel 9.7 Reference Manual