However, a molecular system consisting of many molecules cannot be easily prepared by those editors.
"Packmol" is a good software for readily creating such a large system.
or http://leandro.iqm.unicamp.br/packmol/versionhistory/
1. Install "Packmol" as instructed. (it can easily be built in Cygwin64 console.)
2. Prepare component molecules in pdb, xyz, etc file format.
(component molecules can be DPD structure.)
3. Make an input script
4. Run "packmol < filename.inp"
An example Packmol input script is below:
# Every atom from diferent molecules will be far from each other at least 2.0 Angstroms in the system.
tolerance 2.0
# Coordinate file types will be in pdb format (keyword not required for pdb file format, but required for tinker, xyz or moldy).
filetype xyz
# The output configuration filename
output 100water_5Na_5Cl.xyz
# The first three numbers are the minimum x, y, z coordinates for this molecules, the last three are maximum coordinates.
structure Na.xyz
number 5
inside box 0. 0. 0. 20. 20. 20.
end structure
structure Cl.xyz
number 5
inside box 0. 0. 0. 20. 20. 20.
end structure
structure water.xyz
number 100
inside box 0. 0. 0. 20. 20. 20.
# inside box Xmin Ymin Zmin Xmax Ymax Zmax
# inside box Xmin Ymin Zmin Xmax Ymax Zmax
# inside sphere 10.0 10.0 15.0 8.0
# inside sphere a b c d (a,b,c,d in a sphere equation, (x-a)^2 + (y-b)^2 + (z-c)^2 - d^2 = 0, d is the diameter)
# inside cylinder 0.0 0.0 0.0 1.0 0.0 0.0 5.0 10.0
# inside cylinder x1 y1 z1 x2 y2 z2 d l (direction_of_line_in_vector_(x1 y1 z1 x2 y2 z2), distance_to_the_line_(d), length_of_cylinder_(l))
# inside sphere a b c d (a,b,c,d in a sphere equation, (x-a)^2 + (y-b)^2 + (z-c)^2 - d^2 = 0, d is the diameter)
# inside cylinder 0.0 0.0 0.0 1.0 0.0 0.0 5.0 10.0
# inside cylinder x1 y1 z1 x2 y2 z2 d l (direction_of_line_in_vector_(x1 y1 z1 x2 y2 z2), distance_to_the_line_(d), length_of_cylinder_(l))
end structure
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