Hi Nikola -
Tom, or some of the other guys with a bit more history behind them than I
have will have to give you the lowdown on the mden values, but with regard
to these three values, I see values like that fairly typically, and the
pmemd behaviour replicates sander behaviour. Okay, one last consideration -
are you sure you were pressure-equilibrated before starting nve? (ie., the
system density was not still slowly increasing). That's the only other wild
guess I can come up with off the top of my head. This is really bad temp
conservation, so something is just not right, and I don't see a problem with
your run params.
Best Regards - Bob
----- Original Message -----
From: "Nikola Trbovic" <nt2146.columbia.edu>
To: <amber.scripps.edu>
Sent: Thursday, August 09, 2007 6:50 PM
Subject: Re: AMBER: NVE energy and temperature drift
> 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
>> >
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Received on Sun Aug 12 2007 - 06:07:43 PDT
