ForConXThe force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs AMBER, CHARMM, DLPOLY, GROMACS and LAMMPS. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion.
The idea was born during short term scientific missions of the COST action CM1206 "Exchange on ionic liquids" to our lab. Since the external students use different MD programs to CHARMM, an easy conversion tool to translate force fields was desirable. The increasing number of MD programs argued for a non-pairwise conversion but a more general approach. Consequently, we merged the single conversion tools using the XML file format for storing all force field informations and switched to PYTHON2. This way, new MD programs can be easily added by writing an interface to the XML database.
- This program is free of any warranty. Use at your own risk.
- 100% conversion accuracy is not possible!
- MD programs have different Coulombic prefactors.
- Not all potentials, e.g. harmonic cosine or Morse potentials, are available in all MD programs.
- 1-4 scaling for Lennard-Jones is handled differently. For example, CHARMM allows for particular σ14 (not equal to σ) for two interacting atoms whereas AMBER has a simple scaling factor for ε.
- The numeric precision of the atomic coordinates in the corresponding file is different. ForConX uses the PDB format for conversion which may result in a loss of accuracy during conversion.
- Even if all potentials would be converted with 100% accuracy, there will still be deviations in the MD trajectories due to different shifting and switching functions, thermostats, barostats, assignment of starting velocities, ...
- This program is free of charge and published under GNU general public licence 3.
- This is a program written by students. Further contributions of you is welcomed!
- Please cite
"ForConX - A Forcefield Conversion Tool Based on XML"
V. Lesch, D. Diddens, C.E.S. Bernardes, B. Golub, A. Dequidt, V. Zeindlhofer, M. Sega and C. Schröder
J. Comput. Chem. 38 (2017), 629