How to install Tinker-OpenMM

Overview

Teaching: 5 min min
Exercises: 0 min

Questions

• Install Tinker-OpenMM to Palmetto

Objectives

https://github.com/TinkerTools/tinker-openmm

At time of writing this doc, we need to build Tinker-OpenMM against an OpenMM release from immediately prior to 4 March 2021. Therefore, I build openmm version 7.5.0 using conda environment:

conda install -c conda-forge openmm==7.5.0

Following are steps to install Tinker_OpenMM to Palmetto.

1. Request for a GPU node

2. Load these modules: anaconda3/2019.10-gcc/8.3.1 cuda/11.0.2-gcc/8.3.1 gcc/6.1.0

3. Git clone tinker-openmm: $ git clone https://github.com/TinkerTools/tinker.git

4. Build FFTW Fourier transform : $ cd fftw $ ./configure -prefix==/home/tuev/source/tinker/tinker/fftw $ make && make install

5. Move into the top-level ~/tinker directory, and create a /build subdirectory. $ cd ../ && mkdir build

6. Move into the new /build subdirectory, and copy source and related files via the commands: $ cp ../source/*.f . $ cp ../openmm/ .

7. Edit Makefile with following information: (these are applied to me with tinker home and openmm home):

TINKERDIR = /home/tuev/source/tinker/tinker TINKER_LIBDIR = $(TINKERDIR)/lib BINDIR = $(TINKERDIR)/bin LINKDIR = $(TINKERDIR)

FFTWDIR = $(TINKERDIR)/fftw FFTW_LIBDIR = -L$(FFTWDIR)/lib FFTW_LIBS = -lfftw3_threads -lfftw3

OPENMMDIR = /home/tuev/.conda/envs/openmm750 OPENMM_INCLUDE = $(OPENMMDIR)/include OPENMM_LIBDIR = -L$(OPENMMDIR)/lib OPENMM_LIBS = -lOpenMM -lOpenMMAmoeba

CUDA_DIR = /software/spackages/linux-centos8-x86_64/gcc-8.3.1/cuda-11.0.2-g47zt3sfdo5camhrju5orm5pwkvjf3n2 CUDA_INCLUDE = $(CUDA_DIR)/include CUDA_LIB = $(CUDA_DIR)/lib

1. Run the “make” command to build executables. When the build is finished, there will be three executables produced in the build directory: “analyze_omm.x”, “bar_omm.x” and “dynamic_omm.x”.

Key Points

• Tinker, OpenMM