Dr. Case and Dr. Simmerling,
Thank you both for the helpful explanation! I tried different gamma_ln this
afternoon, and it seems increasing gamma_ln help stablize the temperature a
bit.
Best,
Mingfeng
On 9/21/06, David A. Case <case.scripps.edu> wrote:
>
> On Thu, Sep 21, 2006, Mingfeng Yang wrote:
> >
> > In Amber manual, it's recommended that Langevin dynamics (ntt=3),
> > instead of Berendsen coupling (ntt=1), should be used to control the
> > temperature, especially for GB simulation. However, it seems the
> > temperature fluctuation (20-40) is pretty significant in the case of
> > ntt=3, while it's only ~6 when ntt=1.
> >
> > For example, in my current system (a deca-peptide) simulated with GB
> > model at 300K. The temperature can sometimes jump to >400K. Is it a big
> > deal?
>
> This subject was just discussed recently on this mail-list:
>
> http://amber.ch.ic.ac.uk/archive/200608/0329.html
>
> If you use the formula given there, and assume a molecular mass of 1 kD
> (roughly correct for a 10 residue peptide), then the predicted
> root-mean-square fluctuation in temperature is about 24 degrees. Since
> you
> say you are getting a temperature fluctuation of "20-40", that sounds
> about
> right to me. With this large an rms deviation, seeing an occasional spike
> of 100 degrees is not out of the question.
>
> You might try a gamma_ln of 5-10, just to see if that prevents the really
> big
> spikes (although you still want the rms fluctuation to be something like
> the
> number quoted above.)
>
> As discussed in the earlier mail, fluctuations are inversely proportion to
> the
> size of the system, and can be (and should be) quite large when you have
> only
> a single, relatively small peptide in your simulation. The smaller
> results
> you quote for ntt=1 are a reflection that you are *not* getting a
> canonical
> ensemble with that thermostat.
>
> ...hope this helps....dac
>
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Received on Sun Sep 24 2006 - 06:07:15 PDT
