AMBER Archive (2007)

Subject: AMBER: NVE energy and temperature drift

From: Nikola Trbovic (nt2146_at_columbia.edu)
Date: Thu Aug 09 2007 - 15:24:11 CDT

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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