OpenMM 7.3 beta
Posted: Mon Aug 27, 2018 12:20 pm
A beta of OpenMM 7.3 is now available. Here are some of the most important changes in this version.
There is a new force class called RMSDForce, which computes the RMSD between the current positions and a reference structure over a set of particles. This is intended mainly for use with CustomCVForce. You can use it to implement various types of biasing forces that depend on an RMSD.
We've added new features to CustomIntegrator so that expressions can now involve vector functions such as cross products and dot products. This does a lot to expand the range of algorithms it's possible to implement with a CustomIntegrator.
We've added a lot of new features to the file importers. The CHARMM importer now supports the polarizable force field, and the Gromacs importer supports a larger set of features (functional forms, combination rules, virtual site types, etc.).
NonbondedForce has a new feature that is very useful for alchemical calculations. It can define global parameters, then automatically modify the charges and LJ parameters of particles based on them. In a constant pH simulation, for example, you would have a global parameter for each titratable site, and changing that parameter would interpolate between two states. This is much more efficient than directly modifying the particle parameters, which is what you had to do before.
This release also includes a lot of less visible internal changes. Much of this is to clean up and simplify the code (eliminating thousands of lines in the process). We now require a compiler that supports C++11, and that has enabled a lot of simplification. There also are a lot of changes to improve performance and overall behavior: tuning for Volta GPUs, reducing overhead for CustomIntegrators, making the energy minimizer more robust, improving the performance of custom forces on the CPU platform, and so on.
You can install it with the following command:
That will install a build that was compiled against CUDA 9.2 (and therefore requires you to have CUDA 9.2). If for some reason you need to use a different CUDA version, we now provide Linux and Mac builds compiled against all versions back to 7.5. Just specify a different label when installing. For example, to get a version built against CUDA 9.0 use the command
Please give it a try and let us know how everything works for you.
Peter
There is a new force class called RMSDForce, which computes the RMSD between the current positions and a reference structure over a set of particles. This is intended mainly for use with CustomCVForce. You can use it to implement various types of biasing forces that depend on an RMSD.
We've added new features to CustomIntegrator so that expressions can now involve vector functions such as cross products and dot products. This does a lot to expand the range of algorithms it's possible to implement with a CustomIntegrator.
We've added a lot of new features to the file importers. The CHARMM importer now supports the polarizable force field, and the Gromacs importer supports a larger set of features (functional forms, combination rules, virtual site types, etc.).
NonbondedForce has a new feature that is very useful for alchemical calculations. It can define global parameters, then automatically modify the charges and LJ parameters of particles based on them. In a constant pH simulation, for example, you would have a global parameter for each titratable site, and changing that parameter would interpolate between two states. This is much more efficient than directly modifying the particle parameters, which is what you had to do before.
This release also includes a lot of less visible internal changes. Much of this is to clean up and simplify the code (eliminating thousands of lines in the process). We now require a compiler that supports C++11, and that has enabled a lot of simplification. There also are a lot of changes to improve performance and overall behavior: tuning for Volta GPUs, reducing overhead for CustomIntegrators, making the energy minimizer more robust, improving the performance of custom forces on the CPU platform, and so on.
You can install it with the following command:
Code: Select all
conda install -c omnia/label/beta -c conda-forge openmmCode: Select all
conda install -c omnia/label/betacuda90 -c conda-forge openmmPeter