Re: [AMBER] Potential energy fluctuation of NVT ensemble

From: <diego.soler.uam.es>
Date: Sat, 05 Nov 2016 09:29:38 +0100

Hi,
In the Canonical Ensemble, try to compute the variance of the E. It is
not a hard exercise, but just a straigth-forward application of the
definitions. The result is proportional to the square of the
temperature and to the variation rate of the energy of your system
with respect to temperature.

So, plugging into that some numbers will tell you that, for a system
as big as yours -with all the "noisy" waters etc- and such a high
temperature, 300K, a few hundreds Kcal/mol is about the expected size
of energy fluctuations.

Quoting Zhe Li <zheli.dal.ca>:

> Dear all,
>
> I ran a production NVT simulation and found that the fluctuation of
> potential energy is as large as several hundreds kcal/mol. Is this
> kind of fluctuation normal? The simulation was in water box. At
> first I thought this was because the geometry of the frames was not
> optimized. But after I used Sander to optimize some of the frames
> with ntmin = 3, the large energy difference was still there. I
> visualized the trajectory. It seems that this potential energy
> difference is caused by change of conformations. My calculation is
> on a metalloenzyme after initial equilibration including constrained
> minimization, full minimization, and warming up by a short NPT. The
> input files are attached. If my result is unusual, is there
> something wrong with my input files? Thank you.
>
> Zhe Li
>
>
> Input files:
>
> min1.in
> Initial minimization solvent + ions
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2500,
> ntb = 1,
> igb = 0,
> ntr = 1,
> cut = 8.0
> /
> Hold the substrate fixed
> 500.0
> RES 1 464
> END
> END
>
> min2.in
> &cntrl
> imin = 1,
> maxcyc = 50000,
> ncyc = 25000,
> ntb = 1,
> igb = 0,
> ntr = 0,
> cut = 8.0
> /
>
> eq.in
> 100ps MD with res
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 2, ntp = 1,
> pres0 = 1.0, taup = 2.0
> cut = 8.0,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 2, ig = -1,
> nstlim = 50000, dt = 0.002,
> ntpr = 1000, ntwx = 2000, ntwr = 2000,
> /
> Keep substrate fixed with weak restraints
> 10.0
> RES 1 464
> END
> END
>
> md.in
> 100 ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 1,
> cut = 8.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000000, dt = 0.002,
> ntpr = 10000, ntwx = 10000, ntwr = 10000
> ioutfm = 1,
> iwrap = 1,
> ig = -1,
> /
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Sat Nov 05 2016 - 01:30:02 PDT
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