Tinker-HP is a CPU based, double precision, parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable QM/MM. Tinker-HP is an evolution of the popular Tinker package that conserves it simplicity of use but brings new capabilities allowing performing very long molecular dynamics simulations on modern supercomputers that use thousands of cores. The Tinker-HP approach offers various strategies using domain decomposition techniques for periodic boundary conditions in the framework of the (n)log(n) Smooth Particle Mesh Ewald or using polarizable solvation continuum simulations through the new generation ddCosmo approach. Tinker-HP proposes a high performance scalable computing environment for polarizable force fields giving access to large systems up to millions of atoms.

Running Tinker-HP

To Download Tinker-HP v1.2

wget --no-check-certificate https://tinker-hp.ip2ct.upmc.fr/docrestreint.api/473/8c9b2151cab3a0d442df84ff4228b8dd2fe8b97f/tgz/tinker-hp.v1.2_isc20_competition.tgz

or click here. Basic installation instructions can be found in the readme PDF in the Zip attached.

Basic Installation would be:

./configure ; make -16 ; make install ; cd example ; ./ubiquitin2.run

More tuning options can be found in the PDF.

Output example:

$ ./ubiquitin2.run 

     ######################################################################
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  ###                                                                      ###
 ###            Tinker-HP  ---  Software Tools for Molecular Design         ###
 ##                                                                          ##
 ##                        Version 1.2   November 2019                       ##
 ##                                                                          ##
 ##     Copyright (c) Washington University in Saint Louis (WU)              ##
 ##                   The University of Texas at Austin                      ##
 ##                   Sorbonne Universites, UPMC (Sorbonne)                  ##
 ##                              1990-2019                                   ##
 ###                       All Rights Reserved                              ###
  ###                                                                      ###
   ##########################################################################
     ######################################################################

License Number : ISC20_Competition

Cite this work as :

   Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale
   Simulations of Large Complex Systems with Advanced Polarizable Force Fields.

   Louis Lagardre, Luc-Henri Jolly, Filippo Lipparini, Felix Aviat,
   Benjamin Stamm, Zhifeng F. Jing, Matthew Harger, Hedieh Torabifard,
   G. Andrs Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday,
   Pengyu Y. Ren, Jay W. Ponder and Jean-Philip Piquemal,

   Chem. Sci., 2018, 9, 956-972,  doi: 10.1039/c7sc04531j

 3D Domain Decomposition
Nx =     2  Ny =     2  Nz =     2
 In auto-tuning mode......
 factors:            1           2           4           8
 processor grid           1  by            8  time=  1.399874687194824E-003
 processor grid           2  by            4  time=  1.043856143951416E-003
 processor grid           4  by            2  time=  7.894933223724365E-004
 processor grid           8  by            1  time=  5.473494529724121E-004
 the best processor grid is probably            8  by            1
  
 ***** Using the generic FFT engine *****
  

 Smooth Particle Mesh Ewald Parameters :

    Ewald Coefficient      Charge Grid Dimensions      B-Spline Order

          0.5446               72    54    54                 5

 Random Number Generator Initialized with SEED :          12345
 3D Domain Decomposition
Nx =     2  Ny =     2  Nz =     2

 Langevin Molecular Dynamics Trajectory via BAOAB-RESPA Algorithm

    MD Step      E Total   E Potential     E Kinetic       Temp       Pres

         1   -18699.3485   -27470.3061     8770.9576     302.23    -264.38
         2   -18704.1001   -27478.8942     8774.7941     302.36    -397.49
         3   -18693.6690   -27442.7636     8749.0946     301.47    -184.74
         4   -18691.5564   -27548.0349     8856.4785     305.17    -607.14
         5   -18686.6435   -27364.3032     8677.6597     299.01    -887.84
         6   -18682.8234   -27485.3114     8802.4879     303.31    -927.21
         7   -18682.7029   -27413.0837     8730.3808     300.83    -727.35
         8   -18689.4472   -27494.0409     8804.5937     303.39    -294.13
         9   -18697.8714   -27455.9405     8758.0691     301.78    -566.06
        10   -18694.3349   -27448.8444     8754.5095     301.66    -810.07

For every 100 steps, you will get performance numbers, we will be looking at those.

For example:

Notes

1. Consider changing MPI_INIT_THREAD to MPI_INIT, not using the multi-threading, in case it causes running issues.

Tasks

1. Build and Run Tinker-HP

Build and run Tinker-HP application, you build it however you like and use any MPI. Test it on the examples supplied with the source code.

2. papain and protease_dimer inputs

The Input file for the competition would be some COVID-19 virus proteins and STMV (the complete Satellite Tobacco Mosaic Virus), much larger.

Analyze the papain and protease_dimer from COVID-19 and stmv inputs, run the following mpirun command

For (papain, protease_dimer) use timestep=1000 , STMV use timestep=100.

Submission:

3. Visualisation

Run the papain and protease_dimer benchmarks with the following input parameters, steps=10000 and sf=0.1

Use the *.arc file as an input to VMD or any other tool to visualize the protein movement.

See here for more documentation how to extract image and video.

https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html

Here is an example of the COVID19 protease that looks like heart.

4. Socialize your work

Add your team name or photo to the video and tweet about it using the handles: #ISC20 ISC20_SCC @TINKERtoolsMD. In case you don’t have a team twitter, submit to use the video.

HPC-Works

Tinker-HP Challenge