Hi David,
Try setting dsum_tol = 0.000001 (instead of the default 10-5) in the &ewald
namelist. This can often have a profound effect on energy conservation (to
the point where it should probably be the default if not for 'political'
reasons).
I would also set nscm=0 since having this set to 1000 may be slowly bleeding
energy out of the system.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of David Cerutti
> Sent: Monday, March 17, 2008 17:21
> To: amber.scripps.edu
> Subject: AMBER: What's making my system lose total energy?
>
> I thought that this input would order up a very nice, stable
> simulation
> in the NVE ensemble. Now, I find that the system (256 glycerol
> molecules) is actually losing potential energy at the rate of
> roughly 1
> kcal/60 ps. The typical problem with NVE simulations is that
> they gain
> energy (significantly) if the time step is set too high. But, the
> opposite is true here. The input file:
>
> >>>>>
> An NVE MD run file
> &cntrl
>
> nmropt = 0,
> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 100, ntwx = 10000, ntwv = 0, ntwe = 1000,
> iwrap = 0, ioutfm = 0,
>
> ntf = 2, ntb = 1,
> cut = 9.0,
>
> ibelly = 0, ntr = 0,
>
> imin = 0,
> nstlim = 20000000,
> nscm = 1000,
> t = 0.0, dt = 0.001,
>
> temp0 = 298.15, tempi = 298.15,
> ig = 9376841,
> ntt = 0,
> gamma_ln = 0.0,
> vlimit = 20.0,
>
> ntp = 0, pres0 = 1.0, comp = 44.6,
> taup = 1.0,
>
> ntc = 2, tol = 0.000005, watnam = 'WAT ',
>
> &end
> <<<<<
>
> Note that I have set the SHAKE tolerance to be half the
> default value,
> along with a conservative time step and interaction cutoff.
> Here is some
> sample output:
>
> NSTEP = 100 TIME(PS) = 25182.850 TEMP(K) =
> 307.65 PRESS = 0.0
> Etot = 4401.8340 EKtot = 2659.7186 EPtot
> = 1742.1154
> BOND = 417.5512 ANGLE = 1388.9901 DIHED
> = 601.5975
> 1-4 NB = 363.9760 1-4 EEL = 16825.8254 VDWAALS
> = -2246.5884
> EELEC = -15609.2364 EHBOND = 0.0000
> RESTRAINT = 0.0000
> Ewald error estimate: 0.7533E-05
>
> ...
>
> NSTEP = 106400 TIME(PS) = 25289.150 TEMP(K) =
> 296.16 PRESS = 0.0
> Etot = 4398.9124 EKtot = 2560.4280 EPtot
> = 1838.4844
> BOND = 407.1341 ANGLE = 1415.2345 DIHED
> = 607.2740
> 1-4 NB = 348.7719 1-4 EEL = 16857.0617 VDWAALS
> = -2249.7184
> EELEC = -15547.2735 EHBOND = 0.0000
> RESTRAINT = 0.0000
> Ewald error estimate: 0.2851E-04
>
> Note the difference in the values of Etot. In an earlier run
> with this
> script, I had conducted 20ns of NVE MD (for a diffusion constant
> calculation of the glycerol) and seen the temperature go down
> about 15K
> over the course of the run. Naturally, I assumed that this
> was a problem
> with the system not being settled into a true potential
> energy equilibrium
> at the start of the run, meaning that I would have to run more NPT
> dynamics and then some more NVT to make sure I had the right
> box volume
> and a stable amount of potential energy before starting NVE.
> So, I did
> all that, and found that NVT was giving stable levels of
> potential energy.
> That's when I found that it was this issue of losing TOTAL energy all
> along. Can anyone help?
>
> Thanks!
>
> Dave
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Received on Fri Apr 18 2008 - 21:11:53 PDT
