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Overview

Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs.

Tinker-HP is distributed the Tinker-HP web site, where you can find the latest news, documentation and other useful things.

Usage

Once your account has been enabled to use Tinker-HP (see the license conditions in the Access Prerequisite section) you need to decide on the version of the software you want to use. Use 

$ module avail tinkerhp

to check what versions are available. We normally recommend using the latest version available. For example, to load the version 1.1 of Tinker-HP use 

$ module load tinkerhp/1.1

For more details on using modules see our modules help guide.

Tinker-HP runs under the batch system by using a job script similar to the following example file jobscript:

#!/bin/bash

#PBS -l walltime=1:00:00
#PBS -l mem=250GB
#PBS -l ncpus=96
#PBS -l software=tinkerhp
#PBS -l wd

# Load module, always specify version number.
module load tinkerhp/1.1

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`. Details on:
# https://opus.nci.org.au/display/Help/PBS+Directives+Explained

mpirun dynamic systemName 500 2 1 2 300 > Tinkerhp.out

Where systemName is the name of the files that you want to compute. Tinker-HP needs 2 files to run: .key file that contains a system description and .xyz file that has the system coordinates.


To submit the job to PBS run the command

$ qsub jobscript

License requirements

We give individuals access to Tinker-HP on a per request basis as a condition of our license agreement. Users must apply to the NCI to access this software agreeing to the conditions of use for Tinker-HP as below:

1) Access is for members of academic research organizations only.

2) You should include the appropriate citation in any publications.

a) Any published work which utilizes Tinker shall give appropriate acknowledgement to the Tinker developer community's contribution by including the following main reference:

«TINKER 8: A Modular Software Package for Molecular Design and Simulation, Joshua A.
Rackers, Marie L. Laury, Chao Lu, Zhi Wang, Louis Lagardère, Michael Schnieders, Jean-Philip
Piquemal, Pengyu Ren, Jay W. Ponder, J. Comput. Chem, 2018»

b) Any published work which utilizes Tinker-OpenMM shall give, in addition to the main Tinker reference,
appropriate acknowledgement to the Tinker-OpenMM developer community's contribution by
including the following reference:

«Tinker-OpenMM: Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs.
Matthew Harger, Daniel Li, Zhi Wang Kevin Dalby, Louis Lagardère, Jean-Philip Piquemal , Jay
Ponder, Pengyu Ren, J. Comput. Chem., 2017, 38, 2047-2055.»

c) Any published work which utilizes Tinker-HP shall give, in addition to the main Tinker reference, appropriate acknowledgement to the Tinker-HP developer community's contribution by including the following reference:
«Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of
Large Complex Systems with Advanced Polarizable Force Fields. Louis Lagardere, Luc-Henri
Jolly, Filippo Lipparini,Felix Aviat,Benjamin Stamm, Zhifeng F. Jing, Matthew Harger, Hedieh
Torabifard, G. Andres Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday, Pengyu Ren, Jay.
W. Ponder, Jean-Philip Piquemal, Chemical Science, 2018, 9, 956-972»

3) We are required to inform Tinker-HP group of the names and institutions of users of the software.

4) The Licensee accepts the Software "as is” and understands that it is experimental in nature.

If these license conditions are acceptable you may go to https://my.nci.org.au/mancini/project/tinkerhp and click join.