CHARMM - TechnionYP5779/SimuMole GitHub Wiki

Overview

CHARMM (Chemistry at Harvard Macromolecular Mechanics) is a molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM (quantum mechanics/molecular mechanics), MM/CG , and a range of implicit solvent models. It contains a comprehensive set of analysis and model building tools, and it has community support. We can get the full software for free but without the high-performance MD functionality.

Usage

CHARMM is a command line program that runs on UNIX and UNIX-like systems (e.g., Linux) but not in windows (unless we run it via the CYGWIN emulation layer). In Linux, for example, we can run the command-line (The charmm executable reads input from standard input and writes to standard output by default): charmm -i filename.inp -o filename.out, where:

-charmm is the program name

-filename.inp is a text file contains the CHARMM commands

-filename.out is the log file for the run, which can be controlled so we can get the values for temperature, energy pressure, etc.

There is an option to pass more parameters in the command-line which can be accessed within the input script. As mentioned above, all interactions in CHARMM is done via text commands, mostly written in pre-written scripts (filename.inp). The ordering of commands is limited only by the data required by the command. CHARMM can produce some files that can be input into other programs for visualization or analysis (like VMD).

Conclusion

I am not sure how relevant this program to us. It is possible to build a wrapper in C# to get the wanted calculations from CHARMM (The man here did it years ago in python and java, but I didn't found the code though, only the API), but I am not sure the possibility of it. Moreover, the program is available for Unix systems only, so it can be a problem to use it on windows.

A tutorial can be found here, I read some of it to get a better understanding of CHARMM, but due to lack of knowledge in chemistry, my understanding of how CHARMM works was little.