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Tinker workshop

Speaker: Tinker
Speaker Link: https://tinker-hp.org/
Time: 10:00 CET 10-Feb-2023

This Winter School class is dedicated to the functionalities and the usage of the Tinker modeling package. The Tinker package comes with several programs to run molecular simulations, from system preparation to molecular dynamics up to analysis of the results of such simulations. It has a particular focus on the use of advanced polarizable multipolar force fields such as AMOEBA whose electrostatic interactions include a polarization term modelling the induction response of atomic electron clouds to a fluctuating environment. This higher-resolution description of the molecular interactions comes with a higher computational cost, which is why High-Performance implementations such as Tinker-HP (for CPUs and GPUs) have been introduced. These implementations share the structures of their inputs and outputs and many of their core functionalities. Therefore, this school has a particular focus on Tinker-HP (https://tinker-hp.org/ and https://github.com/TinkerTools/tinker-hp).

The goal here is not to review all of the (many) functionalities of the Tinker programs but to focus on the most basic ones such as system preparation, energy analysis, standard molecular dynamics and simple enhanced sampling simulations. For a more complete description of all these possibilities, one can look at the Tinker user guide available on Jay Ponder’s web page dedicated to Tinker. For the more complex case of the parametrization of a new system with AMOEBA, one can look at the poltype2 program that can handle this procedure systematically.



Video is available only for registered users.

11 thoughts on “Tinker workshop”

  1. Saturday, 11 February 2023 02:03

    Hello, I am trying to install CPU version of tinker-hp. According to the video recorded yesterday, the compilation was done in v1.2 directory. I downloaded all the files using git commands. The files in v1.2 directory from the video are different from those from the github. For example, configure file doesn't exist in the git version. Would you please update the files in github, so that I can proceed compilation and execution of some examples? Thank you for the nice tinker tutorial.  

      1. Sunday, 12 February 2023 14:03

        As you suggested, I ran autoconf ; automake. But the following error message appeared. As this is first time to experience such a problem, please help me to install the tinker-hp successfully. I am using UBUNTU 22.04 version. Thanks.

        ==== Message from autoconf ; automake ======

        kim@AMD1:~/tinker-hp/v1.2$ autoconf ; automake
        aclocal.m4:17: warning: this file was generated for autoconf 2.69.
        You have another version of autoconf. It may work, but is not guaranteed to.
        If you have problems, you may need to regenerate the build system entirely.
        To do so, use the procedure documented by the package, typically 'autoreconf'.
        configure.ac:14: error: version mismatch. This is Automake 1.16.5,
        configure.ac:14: but the definition used by this AM_INIT_AUTOMAKE
        configure.ac:14: comes from Automake 1.13.4. You should recreate
        configure.ac:14: aclocal.m4 with aclocal and run automake again.
        colvars/Makefile.am: error: required file './depcomp' not found
        colvars/Makefile.am: 'automake --add-missing' can install 'depcomp'

        1. Sunday, 12 February 2023 16:26

          you should run "aclocal" and "automake & autoconf" again (see the error message you obtained)

          Then "automake --add-missing" if you have the error about the missing depcomp script again

          1. Tuesday, 14 February 2023 08:23

            Thank you, Louis. With your great help, I managed to compile and execute tinker-hp. But I need to study more to understand all the procedures you explained in the workshop. 

  2. Friday, 10 February 2023 12:12

    Is there any certificate provided who complete the workshop?

    1. Friday, 10 February 2023 13:21

      There are no separate certificates for the workshops...

      1. Friday, 10 February 2023 15:13

        Aah, the full night I was available and complete the qchem workshop if I know you provided recordings I will not attend the seesion. It is somehow unjustify with those people who attend whole session but not get any certificate as previous year you provided ceritificate who attend and complete tha Gaussian session.

  3. Thursday, 09 February 2023 09:34

    Hello, it could be very useful to have the workshop recorded, in order to revisit it, if necessary :)

  4. Tuesday, 07 February 2023 01:14

    Hello, will this workshop be recorded? Could we revisit it?