# Re: [AMBER] Potential energy fluctuation of NVT ensemble

From: Zhe Li <zheli.Dal.Ca>
Date: Sat, 5 Nov 2016 17:30:47 +0000

Hi Neil and Diego,

I have another question. I want to choose some frames as the starting point for my “static” QM/MM geometry optimization to locate a transition state with Gaussian 09. Should I only chose frames with the lowest potential energies? I think this is because according to Boltzmann distribution, the probability to observe the frames with high energies is negligible. Thanks.

Zhe

> On Nov 5, 2016, at 5:29 AM, diego.soler.uam.es wrote:
>
>
> 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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>
>
>
>
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Received on Sat Nov 05 2016 - 11:00:02 PDT
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