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_U1M_allatom_optimized_geometry.lt
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_U1M_allatom_optimized_geometry.lt
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#----------------------------TITLE -----------------------------------------------------------------------------------------
# Methane
#
# This file was generated at 12:03 on 2022-01-01 by
#
# Automatic Topology Builder
#
# REVISION 2021-05-20 12:41:00
#---------------------------------------------------------------------------------------------------------------------------
# Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark
#
# Institute : Molecular Dynamics group,
# School of Chemistry and Molecular Biosciences (SCMB),
# The University of Queensland, QLD 4072, Australia
# URL : https://atb.uq.edu.au
# Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.
# An Automated force field Topology Builder (ATB) and repository: version 1.0.
# Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.
# 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.
# Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.
# DOI:10.1021/acs.jctc.8b00768
#
# Disclaimer :
# While every effort has been made to ensure the accuracy and validity of parameters provided below
# the assignment of parameters is being based on an automated procedure combining data provided by a
# given user as well as calculations performed using third party software. They are provided as a guide.
# The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided
# are appropriate for use in any specific application. Users are advised to treat these parameters with discretion
# and to perform additional validation tests for their specific application if required. Neither the authors
# of the ATB or The University of Queensland except any responsibly for how the parameters may be used.
#
# Release notes and warnings:
# (1) The topology is based on a set of atomic coordinates and other data provided by the user after
# after quantum mechanical optimization of the structure using different levels of theory depending on
# the nature of the molecule.
# (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.
# In these cases alternative type codes are provided at the end of the line.
# (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral
# type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard"
# or "uncertain" in comments.
# (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder
# for those fields that could not be determined automatically. The parameters in these fields must be assigned manually
# before the file can be used.
#---------------------------------------------------------------------------------------------------------------------------
# Input Structure : _U1M_allatom_optimized_geometry.lt
# Output : ALL ATOM topology
# Use in conjunction with the corresponding all atom PDB file.
#---------------------------------------------------------------------------------------------------------------------------
# Citing this topology file
# ATB molid: 15610
# ATB Topology Hash: af5ba
#---------------------------------------------------------------------------------------------------------------------------
# Final Topology Generation was performed using:
# A B3LYP/6-31G* optimized geometry.
# Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.
# Initial charges were estimated using the ESP method of Merz-Kollman.
# Final charges and charge groups were generated by method described in the ATB paper.
# If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.
#---------------------------------------------------------------------------------------------------------------------------
#| Instructions
#| ------------
#|
#| This file can be used as a building block to create LAMMPS systems
#| with the moltemplate.sh program (available at http://www.moltemplate.org).
#| Moltemplate provides a flexible means to build up complex system from
#| molecular template and force field files while avoiding clashes in type
#| numbers for atoms, bonds, etc.
#|
#| Moltemplate takes a LAMMPS-template (LT) file as input, which may itself call
#| on other LT files with an `import file.lt` statement, and generates a LAMMPS
#| input script (typically broken into multiple subscripts) and data file.
#|
#| The following is a simple example of a moltemplate script with the file
#| `GROMOS_54A7_ATB.lt` defining the forcefield `GROMOS_54A7_ATB`, and
#| the `_U1M_allatom_optimized_geometry.lt` file defining the molecule `_U1M`.
#| (Typically "_U1M" is a 4-letter code, such as "54A7", and
#| "_U1M_allatom_optimized_geometry.lt" is something like "54A7_allatom_optimized_geometry.lt".)
#|
#| ```
#| # system.lt
#| # simulation of a single molecule in a box of size 50x50x50 Angstroms^3
#|
#| write_once("Data Boundary") {
#| -25.0 25.0 xlo xhi
#| -25.0 25.0 ylo yhi
#| -25.0 25.0 zlo zhi
#| }
#|
#| write_once("In Init") {
#| # a variable named `cutoff` is required by GROMOS_54A7_ATB.lt
#| variable cutoff equal 14.0 # Angstroms
#| boundary p p p
#| }
#|
#| # import the forcefield file
#| import "GROMOS_54A7_ATB.lt"
#| # import molecule building block file
#| import "_U1M_allatom_optimized_geometry.lt"
#|
#| # create a single copy of this molecule at position 0,0,0
#| mol1 = new _U1M.move(0.0,0.0,0.0)
#| ```
#|
#| See the moltemplate manual for a detailed description of the LT file format.
#|
#| The file `system.lt` can be converted to a LAMMPS
#| input `system.in` and data file `system.data` with the
#| following shell command, assuming that all three LT files
#| `system.lt`, `GROMOS_54A7_ATB.lt` and `_U1M_allatom_optimized_geometry.lt`
#| are located in the current directory:
#|
#| ```
#| moltemplate.sh system.lt \
#| -overlay-bonds -overlay-angles -overlay-dihedrals -overlay-impropers
#| ```
#| (The `-overlay-*` flags are required for cases where multiple bonded
#| interactions involve the same atoms.)
#|
#| To run a LAMMPS simulation, you need to create a file (eg "run.in")
#| containing links to the coordinate, topology, and force-field information
#| created by moltemplate.sh. Then you can run LAMMPS ("lmp_mpi") this way:
#| ```
#| lmp_mpi -i run.in
#| ```
#| At a minimum, the file should probably contain the following information:
#| ```
#| # "run.in" file
#| # Read the files generated by running moltemplate.sh:
#| include system.in.init # I assume your main LT file is named system.lt
#| read_data system.data # If not, change "system" to the name of this
#| include system.in.settings # file (ie. the one you ran moltemplate.sh on).
#| # Simulate the system at 300 degrees Kelvin, saving every 1000 timesteps.
#| minimize 1.0e-3 1.0e-5 100000 400000 # minimization beforehand is optional
#| dump mydump all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
#| fix myfxnvt all nvt temp 300.0 300.0 100.0
#| thermo 100 # Report status every 100 timesteps.
#| thermo_style custom step temp pe ke etotal epair ebond eangle edihed
#| timestep 1.0 # The timestep might need to be adjusted.
#| run 100000 # Simulation duration (in timesteps)
#| ```
#|
#|
_U1M inherits GROMOS_54A7_ATB {
write("Data Atoms"){
$atom:H5 $mol:... @atom:HC 0.130000 9.0350490744E-01 4.8084920538E-03 -6.1664470788E-01
$atom:C1 $mol:... @atom:C -0.520000 -5.3088649151E-06 -5.6886554268E-08 2.9416963272E-07
$atom:H2 $mol:... @atom:HC 0.130000 -1.0476875917E-02 8.8822211312E-01 6.3832306694E-01
$atom:H3 $mol:... @atom:HC 0.130000 -1.0392340011E-02 -8.9798231546E-01 6.2451930726E-01
$atom:H4 $mol:... @atom:HC 0.130000 -8.8257247986E-01 4.9523874660E-03 -6.4620116910E-01
}
write("Data Bonds"){
$bond:b1 @bond:g3 $atom:H5 $atom:C1
$bond:b2 @bond:g3 $atom:C1 $atom:H2
$bond:b3 @bond:g3 $atom:C1 $atom:H3
$bond:b4 @bond:g3 $atom:C1 $atom:H4
}
write("Data Angles"){
$angle:a1 @angle:g50 $atom:H5 $atom:C1 $atom:H2
$angle:a2 @angle:g50 $atom:H5 $atom:C1 $atom:H3
$angle:a3 @angle:g50 $atom:H5 $atom:C1 $atom:H4
$angle:a4 @angle:g50 $atom:H2 $atom:C1 $atom:H3
$angle:a5 @angle:g50 $atom:H2 $atom:C1 $atom:H4
$angle:a6 @angle:g50 $atom:H3 $atom:C1 $atom:H4
}
write("Data Dihedrals"){
}
write("Data Impropers"){
}
}