From: Brian Radak (bradak_at_anl.gov)
Date: Tue Mar 21 2017 - 09:44:52 CDT
There's nothing wrong with NVE as long as that addresses whatever
problem you are interested in.
Some NAMD "gotchas" (these are not defaults)
1) COMmotion should be ON, otherwise the system energy will drift
whenever the run command is called (usually after a restart)
2) zeroMomentum ON might be useful also, if using PME
On 03/21/2017 12:13 AM, Akshay Bhatnagar wrote:
> Dear all
> I have simulated an aspartic acid molecules in 10 different explicit
> solvents. Minimization was done for 1000 steps. Equilibration and
> production run for 10ns. However i had a notion that:
> Equilibration usually have: restraints, temperature control, pressure
> control therfore i used NPT ensemble, and;
> Production run usually have no external controls in simulation,
> therfore i used NVE ensemble.
> I want to know, have i done the simulation correctly, or i should not
> have changed the ensemble for production run?
> Please let me know if there are any references.
> Thank you very much.
> With Regards
> Akshay Bhatnagar
> BITS Pilani Hyderabad Campus
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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