I am generating a POPC bilayer in CHARMM GUI. It generates input file for namd. Can these files be used for a complete namd simulation from minimisation to production? If yes, then how good are the results compared to doing it manually?
Hi Diship,
I don't know how good they are for namd but from my experience I can tell you that for amber they work very well.
Hi Diship,
Charmm-gui input files works very well for NAMD simulation.I am using input files generated by Charmm-gui for NAMD simulation for different systems (for both equilibration/minimization and production runs) and it is working very good. You can increase the steps as you like before running.
I didn't have an issue with the procedure back when I did it for course projects. The main issues that may arise will be because your understanding of the system was incorrect, an inaccurate equilibration procedure to generate the correct ensemble and relax your system, input parameters etc. As long as you do sanity checks along the way such as checking convergence to your force tolerance and a negative energy potential, intensive variable checks (T, P, density etc) and use correct thermostats, barostats you should be fine.
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