TINKER on Biowulf

Quick Links

Tinker is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

References:

Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW Tinker 8: Software Tools for Molecular Design. J. Chem. Theory Comput. 9 October 2018; 14 (10): 5273–5289. https://doi.org/10.1021/acs.jctc.8b00529

Documentation

Important Notes

Module Name: tinker (see the modules page for more information)
Example and test files in: /usr/local/apps/tinker/TESTDATA

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratch:40
[user@cn4338 ~]$ module load tinker
[+] Loading tinker  26.1.2  ... 
[user@cn4338 ~]$ cp -a /usr/local/apps/tinker/TESTDATA/test/water.* .
[user@cn4338 ~]$ potential -k water.tip3p 6 water water n 0.001
     ######################################################################
   ##########################################################################
  ###                                                                      ###
 ###            Tinker  ---  Software Tools for Molecular Design            ###
 ##                                                                          ##
 ##                       Version 26.1   February 2026                       ##
 ##                                                                          ##
 ##               Copyright (c)  Jay William Ponder  1990-2026               ##
 ###                           All Rights Reserved                          ###
  ###                                                                      ###
   ##########################################################################
     ######################################################################
...

Batch job

Most jobs should be run as batch jobs.

Create a batch input file (e.g. cellbender.sh). For example:

 
#!/bin/bash

module load tinker

cd /data/$USERNAME/

potential -k water.tip3p 6 water water n 0.001

Submit this job using the Slurm sbatch command.

sbatch --mem=20g --cpus-per-task=8 tinker.sh