SEGMENT

NAME
SEGMENT - Define the ``solute'' in Hamiltonian SGE simulations.

SYNOPSIS
SEGMENT
....
END

DESCRIPTION
This structured command is used to define the ``solute'' in a Hamiltonian SGE simulation and to assign the scaling factors to the intrasolute, solute-solvent and solvent-solvent interactions. The following subcommands may be specified within SEGMENT:

define, kind

$\bullet$

define n1 n2
The define command is used to crop a piece of solute for Hamiltonian scaling in a SGE simulation. One can use up to a maximum of $10$ define commands, cropping 10 disconnected (non overlapping) part of the solute. $n1$ and $n2$ are the atom indices of the selected solute parts. The numeric order of the atoms is that specified in the topology file (see Section 10.3).

$\bullet$

kind inter_type
Once the ``solute'' has been defined using the define subcommand, the subcommand kind is used to scale the solute-solute, solute-solvent interactions. Possible choices for the string inter_type are intra and inter. intra means that the non-bonded energy scaling (see SETUP command) is applied to the intrasolute non-bonded interactions only, i.e. solute-solvent interactions are not scaled, where by ``solvent'' we mean the actual solvent and the solute atoms which were not selected using the define subcommand. inter scales only solute-non solute (i.e. solvent) non bonded interactions. Intrasolute interactions are NOT scaled if inter is specified. If the subcommand kind is not specified, the ORAC assumes that both solute-solvent and solute-solute interactions are scaled.

EXAMPLES
SEGMENT
   define 1 10
   define 1300 1325
   kind inter
END