Re: AMBER: NVE energy and temperature drift

From: Robert Duke <>
Date: Thu, 9 Aug 2007 18:15:58 -0400

Hi Nikola -
Yes, that seems sort of big. A few months ago I ran a small solvated dna
sample under nve for 5 nsec; I was really comparing other methods to pme,
but for pme (probably with cut 8 or 9, everything else fairly standard) I
only saw a downward temp drift of about 0.2 K in 5 nsec with a total Etot
drop from -87902 to -87948. Did you perhaps dink with the default ewald
params or something? What is the system doing over the 20 nsec if you
visualize it - perhaps something interesting? Others may perhaps want to
share their experiences, but well-adjusted pme simulations are supposed to
be pretty darn good at energy conservation.
Regards - Bob Duke

----- Original Message -----
From: "Nikola Trbovic" <>
To: <>
Sent: Thursday, August 09, 2007 4:24 PM
Subject: AMBER: NVE energy and temperature drift

> Dear amber community,
> I have run a couple of 20 ns NVE simulations of a protein in tip3p water
> with a parallel installation of the amber9 pmemd. I first equilibrated
> the system in an NPT simulation (ntt=1) and then started the NVE
> production runs from different starting structures extracted from the
> equilibrated part of the simulation with
> ntt=ntp=0, ntc=ntf=2, ntb=1 and cut=10.
> Over 20 ns Etot rose absolutely linearly and with barely any random
> fluctuations from ~-76660 to ~-75880. Over the same period the
> temperature rose from an average value of ~300 K to an average value of
> ~305 K. The rms fluctuations of the temperature were fairly constant at
> around 1.5-2 K, but the moving average rose again astonishingly
> linearly, as if I had unwittingly set it to be heated slowly.
> I have combed through the archives and found several threads on energy
> drifts in nve simulations, but none seemed to report such a strong drift
> or a solution that would be applicable in my case.
> If I have missed something obvious I apologize for having wasted your
> time in advance, but I would appreciate any insight on what I am doing
> wrong.
> Many thanks in advance,
> Nikola Trbovic
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Received on Sun Aug 12 2007 - 06:07:42 PDT
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