Is polarizable MARTINI models compatible with atomistic models of protein (hybrid simulation) in NAMD? what considerations should I take for timestep in these cases? I'd appreciate your suggestions and comments with references to topo and par files. Is there a better or coarser model for water that can be used in NAMD? The simulation is aimed at docking analysis.
Abdallah Sayyed-Ahmad
you can look into PACE force field. (Qi, Yifei, et al. "CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations." Journal of chemical information and modeling 54.3 (2014): 1003.)
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Sumith Yesudasan
@Abdallah: Looks like a good tool, though it needs a modified version of NAMD. I will try it out anyway.
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