Amber parameter topology file editor
LESSER GPL LICENSE INFO
Copyright (C) 2010 - 2014 Jason Swails
This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
The fortranformat package is released under the MIT license, Copyright (C)
Brendan Arnold. See fortranformat/__init__.py for more information.
This package is designed to make it safe and easy(er) to rapidly prototype changes to the underlying Hamiltonian in Amber as defined in the parameter-topology file. A full description of its capabilities is described in in the Amber 14 manual (available at http://ambermd.org/doc12/Amber14.pdf). The program is comprised of a command interpreter (with readline support), a GUI-frontend based on Tkinter with clickable buttons for each action, and a flexible Python API whose use follows naturally from the simple command interpreter syntax.
The underlying AmberParm class that ParmEd was built around was augmented with OpenMM support so that it is able to directly create an OpenMM System instance with a call signature almost identical to the one provided in the OpenMM application layer. Improvements implemented here include:
-
Periodic box information is set up from the input coordinate file rather than the parameter-topology file, since that is where the 'preferred' box information is stored in Amber
-
The parameter topology file class can read in both a topology file and a coordinate file at the same time (this is required to set the default box information from the inpcrd file)
-
The restart file class/parser is capable of reading both Amber restarts as well as Amber NetCDF restart files, with the format detected automatically
-
In many cases, System creation is noticeably faster with this class for large systems.
Also included are a handful of OpenMM reporters in the chemistry.amber.openmmreporters module, including:
-
AmberStateDataReporter- Prints state data in standard Amber units (and provides options in the call signature to specify the set of units you want to use) -
RestartReporter- Allows Amber-style ASCII or NetCDF restart files to be written periodically during a simulation. It can either write a series of numbered restarts or continually overwrite the previous one. Fully compatible with all Amber programs. -
MdcrdReporter- Allows Amber-style ASCII trajectory files to be written -
NetCDFReporter- Allows Amber-style NetCDF trajectories to be written
The principle difference between the NetCDF support included here and that included in MDTraj is that the NetCDF parsing here is backend agnostic, supporting the implementations in the scipy, netCDF4, and ScientificPython packages (the first one is written in pure Python and does not require linking to the NetCDF libraries). A default implementation is chosen if no explicit choice is made in the order listed above.
The OpenMM action in ParmEd will read a pmemd/sander-like command-line and an Amber-style input file and run the simulation using OpenMM through the Python application layer with equivalent settings. It includes options to specify the platform and precision model, and also has the option to generate a working Python script that will run the equivalent calculation.
The "energy" action in ParmEd will compute a single-point energy from the loaded coordinates, optionally decomposing the energy contributions into "bond", "angle", "dihedral", and "nonbonded" contributions (finer-grained decomposition of the nonbonded components is not currently possible except for direct/reciprocal decomposition).