Hello, You sent this to the ChimeraX address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> , but maybe you are asking about Chimera (a different program) because it has a Molecular Dynamics Simulation tool. (ChimeraX does not have this tool). However, I do not think you can use the Molecular Dynamics Simulation tool in Chimera for anything this complicated. The tool in Chimera is very simple with few options, and for molecular dynamics calculations it is extremely slow compared to other programs that concentrate on this type of calculation (GROMACS, AMBER, CHARMM, NAMD etc.). The tool in Chimera was developed for small molecules, as mentioned in the help page <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html> ...and not only does it lack fancy options and speed optimization, it cannot do QM/MM, which is needed for chemical reactions like proton transfer. You would need to use some other program. The paper methods section (in the link that you sent) says that they used the program NAMD2. In the future, if you have a Chimera question please send it to the Chimera address chimera@cgl.ucsf.edu. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 15, 2024, at 11:59 PM, SAWABE Tomoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

To whom it may be concerned, Thank you so much for developing excellent program for analyzing protein structures. I found Chimera could do molecular dynamics simulations. If I do MD to predict proton paths described in https://www.pnas.org/doi/epdf/10.1073/pnas.1706278114, please teach me which tool we can use. Best Tomoo Sawabe Hokkaido Univ.