NVE simulations in NAMD - the right choice of timesteps and parameters

From: Harish Srinivasan (harishlglk1992_at_gmail.com)
Date: Tue Nov 29 2016 - 04:54:32 CST

I am trying simulate micellar systems like SDS, SDBS micelle in water. I
equilibrated the system for 20 ns using NPT Langevin piston.
Even after 20 ns run, the average temperature remained at 295 K for the
system (I am still pondering why this happened), so I used rescale velocity
(with rescalefreq 2 timesteps) for 500 ps.

 After this I ran a NVE simulation (meaning, i switched off all the
thermostats and barostats) for about another 20 ns, the total energy of the
system seemed to change about 20000 units in the span of 20 ns.

I am using 1 fs timestep, with 2fs for non-bonded forces and 4fs for full
electrostatics. No rigidity imposed.

Thank you,

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