On Fri, Feb 24, 2012 at 2:35 PM, amir abbasi <amir-abbasi.hotmail.com>wrote:
>
> Hi!
> I'm trying to simulate a small nucleic acid molecule (5 nt) in implicit
> solvent and constant temperature (300 K).
> But i got a broad range of temperature from 250 K to 350 K.
> Why?
Because your system is very small. As the number of particles drops, the
size of temperature fluctuations jump.
And How i can solve this problem?
>
Why do you say this is a problem? What is your average temperature over
the whole simulation? If you simulate in explicit solvent, your
temperature fluctuations will drop. You can try playing with various
thermostats (e.g. anderson, berendsen, or langevin) and temperature
coupling constants, but you should be aware of the shortcomings/properties
of each (for example, berendsen does not actually sample rigorously from
the canonical ensemble).
> This is my MD input file:
> &cntrl
> imin = 0,
> ntb = 0,igb=1,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300, temp0 = 300,
> nstlim = 100000000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 1000
> cut = 12.0
>
This is a _very_ small cutoff for implicit solvent calculations. It could
be that your system is smaller than 12 Å, but I would still suggest that
this value should be considerably larger. I don't know how much of an
effect this will have on your temperature fluctuations.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Feb 24 2012 - 12:30:02 PST
