Dear Bob and Tom,
first of all thanks for getting back to me so quickly. I'm not aware of
having made any changes to the ewald parameters. Here's my input file
for the nve production run:
MD run
&cntrl
ntx=5, irest=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500, ioutfm=1,
nstlim=2500000, dt=0.002,
ntt=0, ntp=0, ntc=2, ntf=2,
ntb=1, cut=10.0,
/
To Bob's question I can say that the system doesn't seem to be doing
anything interesting over the 20 ns when visualized. The rmsd over the
trajectory looks fine, the protein stays folded... is there something
else I could look for?
To Tom's final question I can say that yes, the potential energy also
increases linearly from ~-95300 to ~-94800 over the 20 ns. What does
that indicate?
I will try out Tom's suggestions right away, but I wanted to answer your
questions and also share another observation that surprised me, to say
the least: the mden file shows the solute temperature always to be equal
to the overall temperature, while the solvent temperature value is
around -.77E+11. Is that normal? Is it just a bug, or is it something I
have to worry about?
Thanks for your help,
Nikola
On Thu, 2007-08-09 at 18:15 -0400, Robert Duke wrote:
> 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" <nt2146.columbia.edu>
> To: <amber.scripps.edu>
> 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
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
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 - 06:07:43 PDT
