Hi Neha,
~5 degree fluctuations in temperature sound pretty standard for systems in
explicit solvent with a stochastic thermostat (i.e. Andersen or Langevin).
I'm actually a little surprised that your fluctuations are as high, as I
would have expected Berendsen fluctuations to be a bit lower.
It is probably worth mentioning that pressure control in AMBER uses the
Berendsen barostat, which does NOT produce the NpT ensemble. Much like the
Berendsen thermostat, it merely keeps the related microscopic quantity near
the target value, but does not generate the correct distribution. This is
perfectly adequate for generating sensible densities near the NpT average
and is thus fine for equilibration, but I would not recommend using it for
long production runs, especially if you are interested in fluctuations
(they will simply be wrong).
Regards,
Brian
On Mon, Mar 4, 2013 at 9:50 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear list,
>
> We are studying protein phosphorylation (30 amino acids) structures with MD
> simulations. We carried out simulations under the NPT ensemble with AMBER
> 12 PMEMD, cuda version. The temperature vs time plot shows that the
> temperature fluctuates about 6 degrees plus/minus the initial temperature
> which is 310K.
>
> Is the 5 degrees fluctuation a kind of reasonable range in the NPT
> ensemble?
>
> Here is the input file:
>
> Title
>
> &cntrl
>
>
> irest=1,ntx=5,
>
>
> nstlim=5000000,dt=0.002,
>
>
> temp0=310.0,ntt=1,tautp=1.0,
>
>
> ntc=2,ntf=2,
>
>
> cut=10.0,
>
>
> ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
>
>
> ntb=2,ntp=1,pres0=1.0,taup=1.0,
>
>
> ipol=0,igb=0,
>
> ntr=0,
> iwrap=1,
> &end
>
>
> Waiting for your inputs,
>
> Cheers,
> Neha
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Received on Mon Mar 04 2013 - 09:00:03 PST
