AMBER Archive (2004)

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

From: Martina Roeselova (
Date: Fri Jan 23 2004 - 20:16:32 CST


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.

-------- Original Message --------
Subject: NVE & polarizable force field
Date: Thu, 22 Jan 2004 11:05:46 -0800
From: Martina Roeselova <>

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:

         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
         a=30., b=30., c=100.

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