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

From: Felipe Merino (
Date: Tue Nov 29 2016 - 07:03:45 CST


Using multi-timesteps can be quite aggressive. Usually you don't see
this change in energy because of the themostat, but in the NVE
simulations they appear immediately. Why do you want to run NVE anyways?

In any case, try for example using 2fs for everything and you'll see
that the simulation becomes better behaved. Whether or not this is
advisable for you depends on what you are trying to obtain from the
simulation in the first place.


On 29/11/16 11:54, Harish Srinivasan wrote:
> 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,
> Harish

Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2315

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