Share 
Follow 
AboutDownloadsDocumentsForumsSource CodeIssues
Image not available
A MD/GCMC OpenMM/XML interface
Code reads CHARMM-formatted PSF/PRM (tested with CHARMM27, CHARMM36 and C36 CGENFF parameters) and runs MD and enhanced sampling techniques like aMD w/ dihedral boost potential and umbrella sampling. It has implementations of Generalized Born using CustomGBForces in OpenMM too (OBC2 model and GBn2 models) for implicit solvent simulation, and writes output trajectories in DCD format. The GCMC implementation currently requires updates to the OpenMM header (".h") files and is disabled by default, and relies on an MD integrator (Verlet) for NVT simulations between GCMC insertion/deletion moves. Some example programs are provided to build systems from a copy of a single molecule (PSF and PDB with parameters) to simulate increasing solute concentration for self-assembly. XML serialization provides a simple way to interface with CHARMM outside of the package. The OpenGL visualization is shown in the picture and similar to the one provided in other programs here. Run "make" to compile simulation code (OpenMM path is just specified in the Makefile), and in visualizer folder run "make linux" or "make osx" for your platform and then run it with "visualizer 7001" in a spare terminal for the server to come up with the OpenGL display server on TCP port 7001. Hostname and port can be changed and are 'localhost' and 7001 by default in the simulation code right now. It also makes a fun educational tool for watching simulations as they minimize and then run! Simplest options right now are in runmd.cpp and the syntax is "runmd system.psf system.pdb par_file1.prm par_file2.prm par_file3.prm..." and it's mostly focused on infrastructure for building models to run with OpenMM and approaches that can interface with it and to add functionality needed for some of my work. CHARMM/OpenMM work is one potential application. Additional codes as well as new developments for GCMC simulations using the OpenMM libraries, in preparation.
OpenMM CHARMM interface
Feb 21, 2014

version 0.90 - Addresses CHARMM/OpenMM interface directly using XML serialization. Notes  View License

Download Links

Jul 17, 2014
2 MB
Any
Source code


Image not available
Ion MC
This program is similar to ISIM and allows for probing ion environments around biomolecules with periodic boundary conditions or a spherical cell. The hard sphere model is currently used in the implementation but tools for the other available codes can be integrated. The example source shows a dsDNA molecule (1DNA.pdb) in PQR format.
mcion
Feb 03, 2014

Open source C/C++ implementation of ion MC for biomolecules, uses input format of PDB as PQR file (charges and radii)Notes  View License

Download Links

Feb 03, 2014
1 MB
Any
Source code

PLEASE CITE THESE PAPERS

Free Energy Monte Carlo Simulations on a Distributed Network, LNCS 2012 (2011) View


Image not available
LMC GCMC code
This is for treating ions and lipid aggregation with molecule GCMC. The implementation contains some documentation and would serve as the basis for a complete code release, it implements coarse-grained and united atom models (and hybrid CG/united atom models) for molecules with Gaussian, Weeks-Chandler-Andersen, multipole/mixed power and standard LJ/electrostatic potentials etc. Current version is 0.9
LMC GCMC
Feb 03, 2014

Molecule and protein-DNA GCMC  View License

Download Links

Feb 05, 2014
800 KB
Any
Source code
gcmc code, README file inside


OpenMM Constraint Plugin
This plugin adds functionality for harmonic constraints on quantities that are not provided through the OpenMM package. The material is meant to be similar to the "Colvars" modules used in programs such as NAMD and LAMMPS to perform techniques like Umbrella Sampling, Steered Molecular Dynamics, ABF, and Metadynamics.
GroupConstraint.tar.gz
Feb 27, 2014

  View License

Download Links

Feb 27, 2014
57 KB
Any
Source code


Image not available
Wang and Landau MC
This package implements the solution to the boundary condition problems for CG DNA models using the Wang and Landau reaction coordinate method.
WLMC-standalone
Feb 03, 2014

A standalone distribution of the Wang and Landau algorithm (single random walkers) solving the boundary condition problems.Notes  View License

Download Links

Feb 03, 2014
111 KB
Any
Source code

PLEASE CITE THESE PAPERS

Free Energy Monte Carlo Simulations on a Distributed Network (2011) View


Image not available
wlmc-circle
A Wang and Landau sampling method for circular or constrained DNA with a fixed linking number, it utilizes the client/server architecture and the packages are together. The treatment include dsDNA and explicit ions as well as simple screening (Debye) terms.
wlmc-circle
Feb 04, 2014

Constrained DNA with explicit ionsNotes  View License

Download Links

Feb 04, 2014
83 KB
Any
Source code

Feb 04, 2014
157 KB
Any
Source code
Server code, set port number, default 7000

PLEASE CITE THESE PAPERS

Free Energy Monte Carlo Simulations on a Distributed Network (2011) View


Image not available
WLMC client and server model
This one is for solving the DNA condensation problem (multivalent counterions), similar to the computational work of Mark Stevens and intended to fit experimental data from Victor Bloomfield. The program is a client that communicates with the server package.
wlmc-screened
Feb 03, 2014

Screened (Debye or Debye+Manning) electrostatics and explicit ions for dsDNA.Notes  View License

Download Links

Feb 03, 2014
838 KB
Any
Source code

Feb 03, 2014
157 KB
Any
Source code
Server code

PLEASE CITE THESE PAPERS

Free Energy Monte Carlo Simulations on a Distributed Network (2011) View


Feedback