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

From: Brian Radak (
Date: Tue Nov 29 2016 - 12:52:15 CST

On 11/29/2016 10:16 AM, Axel Kohlmeyer wrote:
> On Tue, Nov 29, 2016 at 5:54 AM, 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.
> 1 fs is far too large a time step for unconstained hydrogen atoms. try
> something in the range 0.25 - 0.5fs
> axel.
I'm not sure I fully agree with this. In the absence of multiple
timestepping I've generally experienced quite stable energy conservation
on the order of nanoseconds (and probably longer) when integrating
"floppy" hydrogens with a 1 fs timestep.

That being said (and as Vlad pointed out), I have never not used rigid
water constraints, as those are essentially a non-negotiable feature of
the model. If you have floppy water too, then I would not be terribly
surprised to see 1 fs cause problems.

>> Thank you,
>> Harish

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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