AMBER Archive (2003)

Subject: Re: Etot is not constant in NVE ensemble

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Fri May 09 2003 - 18:20:24 CDT

Dear Hungie
you can do one of two things. either explicitly enter the value
ew_coeff = ... in ewald namelist, or just do as cheatham suggests and
lower the value of dsum_tol in the same namelist. The value determined by
dsum_tol and cutoff is spit out in the mdout file
something like:
     Ewald Coefficient = 0.34864
In this case I might suggest increasing by ~0.5. If you enter a value for
ew_coeff sander won't calculate it from dsum_tol and cutoff. If you don't
enter it sander will calculate.

probably better to follow cheatham's advice and simply set dsum_tol to
0.000001

Good luck
Tom D

 On Fri, 9 May 2003, A.
Hungie wrote:

> Dear Prof. Tom Darden and amber users,
>
> Thank you very much for your response. However, I am still confused. I also
> have no idea what value of ewald coefficient (ew_coeff ) should be used or
> increased. By default, ew_coeff is determine by dsum_tol and cutoff. So how
> to calculate ew_coeff? In my case, if dsum_tol = 0.00001 and cutoff = 8.0
> Angstrom, what is the value of ew_coeff? If I know ew_coeff in this case, I
> may know how large of ew_coeff should be explicitly entered in my input file
> (to get rid of energy drift).
>
> Thank you again in advance.
>
> Best Regards,
> Hungie
>
>
>
> >For comparison I have run a water box of 216 molecules for 5ns NVE with
> >either a 2fs or 1fs time step with standard default. I got a drift of
> >~2kcals per mole out of ~1750 kcals with a 2fs time step and ~1/2 kcal per
> >mole with a 1fs time step. This latter number is comparable to yours
> >relative to total energy. Also note that the energy conservation behaved
> >quadratically with respect to timestep. This does not happen when
> >you have a serious energy drift problem. However if you're unhappy with
> >your results....
> >Tom Cheatham (he can agree/disagree) had a similar problem and found that
> >by increasing the default ewald coefficient a bit he got rid of the
> >drift. It might be that for highly charged systems the discontinuity in
> >direct sum energy/forces at the cutoff [i.e. erfc(beta*r_cutoff)/r_cutoff
> >is too large] could cause heating. By increasing beta (ewald coefficient)
> >this problem is alleviated. I don't recall how much Tom C increased beta.
> >To be correct [i.e. keep a low error vs exact ewald] you then need to
> >increase reciprocal sum parameters slightly. However since the
> >reciprocal pme sum is smooth (no discontinuities) it doesn't seem to me
> >that the reciprocal sum can cause heating. That is your problem is
> >probably due to direct sum discontinuities and can be helped by increasing
> >beta.
> >
> >Hope this help
> >Tom Darden
> >
> > On Fri, 9 May 2003, A. Hungie wrote:
> >
> > > Dear All,
> > >
> > > I have run MD simulation of 14 basepairs DNA (in water and nuetralized
> >by
> > > Na+ ions) using protocol as in Amber tutorial. After doing 6 rounds of
> > > minimizations (reducing restrain energy from 25 to 0 kcal/mol.A^2), I
> >ran MD
> > > in NPT ensemble for 100 ps which I obtained canstant box size. Then I
> > > switched to NVE ensemble for 5.6 ns (800 ps for each run). I found that
> > > total energy is not constant, i.e. it increases about 6 kcal/mol (from
> > > -37828 kacl/mol to -37822 kcal/mol) within 5.6 ns. I used Amber 6 on
> >Linux
> > > cluster and input file as below.
> > >
> > > Is the obtained total energy normal and acceptable? Is it equilibrium?
> > >
> > > #my input file.
> > > ------------------------------------------
> > > &cntrl
> > > ntx = 7, irest = 1, nmropt = 0,
> > > imin = 0,
> > > maxcyc = 1000, ncyc = 5000,
> > > ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
> > >
> > > nstlim = 800000,
> > > dt = 0.001, ndfmin = 0, t = 0.0,
> > > timlim = 999999., ntcm = 1, nscm = 2500,
> > >
> > > ntpr = 1000, ntwr = 1000,
> > > ntwx = 1000, ntwv = 0, ntwe = 0,
> > > ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
> > >
> > > cut = 8.0, dielc = 1.0, nsnb = 10,
> > > scnb = 2.0, scee = 1.2, iwrap = 0,
> > >
> > > ntb = 1, ntp = 0, npscal = 1,
> > > pres0 = 1.0, comp = 44.6, taup = 2.0,
> > >
> > > ntc = 2, tol = 0.000001,
> > > ntf = 2,
> > >
> > > ibelly = 0, ntr = 0,
> > >
> > > temp0 = 300.0, tempi = 300.0,
> > > ig = 71277, heat = 0.0, tautp = 4.0,
> > > ntt = 0, vlimit = 20.0, dtemp = 1.0,
> > > &end
> > >
> > > &ewald
> > > a = 42.0151161, b = 43.0746222, c = 69.8275997,
> > > alpha = 90.000, beta = 90.000, gamma = 90.000,
> > > nfft1 = 45, nfft2 = 45, nfft3 = 72,
> > > order = 4, dsum_tol = 0.00001, eedmeth = 1,
> > > opt_infl = 1, vdwmeth = 1, use_pme = 1,
> > > frc_int = 0, nbflag = 1, skinnb = 1.0
> > > &end
> > > -----------------------------------
> > >
> > > Thank you very much in advance.
> > >
> > > Hungie
>
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