From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Oct 20 2014 - 22:15:59 CDT
Dear NAMD users,
I am currently doing MDFF simulations to investigate some conformations of a protein. The simulation was done in a water box and with a low-resolution electron density map (14A). The system is quite large (>1M atoms) so I have just run for several ns.
By analysing RMSD and CCC of the simulation results, the system seems to converge in the first 2 ns. However the CCC of the system relative to the density map started at 0.60 and converged at 0.65 which was sadly not much improvement. I have step-wisely increased the g-scale value from 0.5 to 3.0 and the CCC further improves to 0.69. After that, I am not able to increase the g-scale value as the simulation will be terminated due to “atom moving too fast” (I guess it was due to the increasing magnitude of the additional potential right?). I understand that such a low-resolution density map will definitely limit the maximum CCC that I can have but is there any other ways to improve the MDFF results?
I will greatly appreciate that if anyone could share your experience on this.
Thanks in advance.
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