AMBER Archive (2004)

Subject: Re: AMBER: Fwd: NVE & polarizable force field]

From: Byungchan Kim (
Date: Fri Jan 23 2004 - 20:58:04 CST


My answer might not related to AMBER itself. I would like to describe the
problem in general way. Because I am not familiar how AMBER deal with
Polarizable force field, I will assume it uses Car-Parinello integrator
for dipoles.

1. I guess this is related to constraint of POL3. Usually, total energy of
constraint NVE dynamics tends to cool during the simulation. So you might
see the drift of total energy. But the energy should be very small
compared to total energy.

2. As I assumed, if Amber use Car-Parinello (Extended Lagrangian) method,
in each timestep it would not be in the real Born-Oppenheimer surface
Your potential would fluctuate around BO. However,
the very beginning of the simulation, I guess the program should solve the
equation iteratively and that is the correct BO. In summary, at the end of
previous simulation, the system is near of BO, but the very beginning of
the next simulation is on the BO. That may give difference of potential

Above is just my opinion without any information about AMBER
implementation. So.. likely incorrect.

Good luck

 On Fri, 23 Jan 2004, Martina Roeselova wrote:

> Hi,
> I am not sure if my email got through. I have't received any answer and
> it haven't found it in the Amber reflector archive either. This time, I
> am trying with no figure attached.
> M.R.
> -------- Original Message --------
> Subject: NVE & polarizable force field
> Date: Thu, 22 Jan 2004 11:05:46 -0800
> From: Martina Roeselova <>
> To:
> Hi AMBER users,
> I run simulation of a water slab using polarizable potential (POL3).
> I use 3D periodic boundary conditions to construct the slab geometry. My
> simulation box is 30-by-30-by-100 Angstroms and contains 864 waters. The
> cutoff is 12 Angstroms. I use Ewald. (see the imput file below)
> I noticed few things that I find disturbing:
> (1) Total energy drift during NVE run: Etot (as printed in mdout file)
> goes down steadily. The NVE simulation was started from a restart file
> produced by a previous 0.5 ns NVT run.

> (2) Discontinuity after restart: After restart of NVE run, there is an
> abrupt drop in total energy Etot (mainly due to the drop in potential
> energy EPtot) compared to the values corresponding to the last step of
> the previous NVE run that was used for restart. In the first few ps, the
> total energy goes up, ABOVE the Etot value of the final step of the
> previous run, and then starts going down again (see attached figure -
> please note the difference in the energy scales for total energy as
> opposed to kinetic and potential energy).
> I see the same discontinuity when restarting a NVT run. It is of the
> same size as in the NVE case, however, it is still much smaller than the
> size of the energy fluctuations during the NVT run - and there does not
> seem to be any drift.
> Is it possible that (1) and/or (2) are somehow related to the use of
> polarizable potential, i.e. the way the dipols are propagated?
> Thanks for any hints/comments/explanations.
> Martina Roeselova
> here is the input file:
> &cntrl
> imin = 0
> irest = 1, ntx = 7
> nstlim= 1000000, dt=0.001
> ntb=1, ipol=1
> ntxo = 1, iwrap=0
> ntpr=1000, ntwx=1000, ntwv = 1000, ntwe=0, ntwr=1000
> ndfmin = 0,ntcm = 0,nscm = 9999999
> ntt = 0, temp0 = 300.00, tautp = 0.2, dtemp = 999.
> cut =12.
> ntc=3, ntf = 3
> maxcyc = 9999,ncyc = 250,ntmin = 1,dx0 = 0.010
> dxm = 0.02,dele = 0.01,drms = 0.00010
> &end
> &ewald
> a=30., b=30., c=100.
> &end
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