This is normal. The size of the fluctuation is roughly proportional to the
number of atoms in your system. If run a simulation of a pure water box,
you'll find a similar result.
--Niel
On Fri, Nov 4, 2016 at 3:15 PM, Zhe Li <zheli.dal.ca> wrote:
> 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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Received on Fri Nov 04 2016 - 17:30:02 PDT
