Dear Bill and Carlos,
Thank you for your suggestions. Actually I
was going through the tutorial "Loop dynamics of the HIV-1 integrase core".
In the equilibration section it is written that
"Some protocols call for very elaborate procedures involving gradually
increasing temperature in a step-wise fashion while other more aggressive
approach simply use a linear temperature gradient and heat the system up to
the desired temperature."
"In the first stage, we will start the system from a low temperature of 100
K and gradually heat up to 300 K over 10 picosecond of simulation time."
I am just confused that the procedure followed here is of the first kind or
second kind i.e. step-wise fashion or aggressive approach.
On Fri, Jan 7, 2011 at 2:00 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
> > tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
>
> irest=0 means start with no velocities from file (0K).
> tempi=100.0 means initialize random velocities to 100K
> temp0=300.0, tautp=2.0, means warm to 300 'quickly'.
>
> This is not a good equilibration protocol for anything but a
> small molecule, since rapid warming will disturb the structure
> of anything large. See the tutorials for other warming schemes.
>
> Bill
>
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--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Fri Jan 07 2011 - 21:30:04 PST
