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


Code Block
languagebash
#!/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


Code Block
languagebash
$ 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.