AMBER Archive (2007)

Subject: Re: AMBER: NVE energy and temperature drift

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Aug 10 2007 - 04:10:51 CDT

Sorry .. the correct reference to my first message is

http://amber.ch.ic.ac.uk/archive/200603/0160.html

vlad

Nikola Trbovic wrote:

>Hi Bob,
>
>The density looks perfectly equilibrated around 1.01 (rmsd of 0.0013 over
>the relevant 1 ns of equilibration). But the PRESS value in the output
>varies wildly around zero with an rmsd of 127. Is that the pressure and is
>that behavior normal?
>
>On the note of mden values I found the relevant thread shortly after I sent
>out my last email, so I know now that amber8 and amber9 simply don't
>distinguish between solute and solvent temperature anymore. But is there
>still a simple way to calculate these values? I'm just curious whether both
>solute and solvent follow the overall heating equally, since I only used a
>weak thermostat (ntt=1).
>
>Many thanks again,
>Nikola
>
>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
>Robert Duke
>Sent: Thursday, August 09, 2007 7:44 PM
>To: amber_at_scripps.edu
>Subject: Re: AMBER: NVE energy and temperature drift
>
>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_at_columbia.edu>
>To: <amber_at_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_at_columbia.edu>
>>>To: <amber_at_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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>
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Dr. Vlad Cojocaru

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