VCM is a software package written in C++. It currently runs on MacOS and Linux. To build it you need a c++ compiler (g++, llvm, etc). VCM uses OpenMM as its main engin. If you don't have OpenMM please read the next section. If you already have OpenMM installed, you need to:

STEP 1: Install the Boost library

STEP 2: Clone the VirtualCellModel project from our github page.

STEP 3: Change directory to VirtualCellModel.

STEP 4: Run makefile by typing 'make'. You may need to modify the make file depending on the openmm installation directory on your machine if OpenMM is installed in a differnet directory than /usr/local/openmm/.

STEP 5: Run ./VCM -h for help.

Update VCM

To update VCM:

STEP 1: Delete the binary output file

STEP 2: Enter:

make clean;make -j4

OpenMM

The Vertual Cell Model package takes advantage of OpenMM as its main molecular dynamics engine. Please use the instructions on the OpenMM webpage to install OpenMM.

Note: Please install the C++ API. If you have already installed OpenMM with 'Conda' on your system you still need to install the C++ API from the source code (more information on OpenMM website). You may need to install additional software packages (OpenCL, FFTW,SWIG, etc) depending on your choice of platforms (GPU, CPU).