SEGMENT

NAME
SEGMENT – Define the “solute” in solute tempering simulations.

SYNOPSIS
SEGMENT
....
END

DESCRIPTION
This structured command is used to define the “solute” in the a solute/tempering REM simulation and to assign the scaling factors for the Hamiltonian REM simulation (see Sec. 5.2) to the intrasolute, solute-solvent and solvent-solvent interactions. The following sub-commands 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 REMD simulation. One can use up to a maximum of $10$

define commands, cropping 10 disconnected (non overlapping) part of the solute. $n1$

and

are the atom indices of the selected solute parts, The numeric order of the atoms is that specified in the topology file (see Sec. 10.3.

$\bullet$

kind inter_type
Once the “solute” has been defined using the define sub-command, the sub-command 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 sub-command. inter scales only solute-non solute (i.e. solvent) non bonded interactions. Intrasolute interactions are NOT scaled if inter is specified. If the sub-command kind is not specified, the ORAC assumes that both solute-solvent and solute-solute interactions are scaled. N.B. When using SEGMENT strecthing and bending are not scaled.

EXAMPLES

Example 1. Here we define the solute from atoms 1-10 and 1300-1325. We only scale the intermolecular solute-solvent with a minimum scale factor of 0.2 (corresponding to a “temperature” of 1500 K). N.B.: In the “solvent” all the atoms of the system are included except for atoms 1-10 and 1300-1325.
```
  SETUP 1.0 1.0 0.2 
  SEGMENT 
    define 1 10 
    define 1300 1325
    kind inter
   END
```
Example 2. Here we scale all the intramolecular interactions for the atoms 1-6 and 101-106. Note that the first argument of the SETUP command (0.1) refer to the scaling factor of the proper torsions involving hydrogen atoms and of the improper torsions. Stretchings and bendings are never scaled when using SEGMENT.
```
  SETUP 0.1 0.1 0.2 
  SEGMENT 
    define 1 6 
    define 101-106  
    kind intra
   END
```

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