COORDINATES

NAME
COORDINATES - Define the coordinates of a solute.

SYNOPSIS
COORDINATES filename

DESCRIPTION
Read the coordinates of the solute (in PDB format) form file filename. This command is best used when also the solvent atoms must be read in.

EXAMPLES

 
&SETUP
   CRYSTAL  20.00  20.00  20.00  90.0  90.0  90.0
#  REPLICATE 2 2 2
&END
&SOLUTE
   COORDINATES  solute.pdb
#  SPACE_GROUP  OPEN benz.group P 2/c
&END
&SOLVENT
   CELL SC 
   INSERT 1.5
   COORDINATES  solvent.pdb
   GENERATE RANDOMIZE  4 4 4
#  GENERATE RANDOMIZE  8 8 8
&END

In this example the coordinates of the solute are read in form the file solute.pdb while the coordinates of the solvent molecule (see &SOLVENT) are read in form the file solvent.pdb. As is now, this input would produce in a box of $20\times 20\times 20$ Å$^{3}$, 1 solute along with 64 replicas (see command GENERATE(&SOLVENT) of the solvent molecule. Of this 64 molecule, those that overlap with the solute molecule (see command INSERT(&SOLVENT) ) are discarded. If the second line in the environment &SOLUTE is uncommented, the solute is assumed to be arranged in the MD box according to the space group specified by the SPACE_GROUP directive. In the present example the group contains 4 molecules per unit cell. So 4 molecules of solute are arranged in the box according to the P 2/c space group along with 64 replicas of solvent molecules. Again the overlapping solvent molecules (say $n_o$) will be discarded. If we comment the line GENERATE RANDOMIZE 4 4 4 and uncomment the lines # GENERATE RANDOMIZE 8 8 8 and # REPLICATE 2 2 2 we double the size of the sample: we will have 8 cell of $20\times 20\times 20$ Å$^{3}$ each with 4 molecules of solute and $8\times 8\times 8 = 512$ solvent molecules minus $8\times n_o$ overlapping molecules.