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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 12 2007 - 06:07:41 PDT
