On 12/14/12 12:40 PM, Dr. Vitaly Chaban wrote:
If you have a correct temperature for the particle of interest,
everything is correct.
One important caveat, of course, is a given thermostat's ability to produce
velocities that belong to a real NVT ensemble. This is not the case, for
instance, with the Berendsen algorithm. It maintains the temperature, but the
distribution is not canonical. If the goal is simply to heat up a given species
and then proceed with further simulations, the method chosen during heating is
probably rather insignificant.
-Justin
On Fri, Dec 14, 2012 at 6:38 PM, tarak karmakar <tarak20...@gmail.com> wrote:
Thanks Dr. Vitaly
Yeap !
From that point of view I'm seeing the correct temperature drift and
it reaches nicely to 300 K after say, 300ps.
But is it a good integrator ( SD ) to perform this job ? Or, should I
opt for other, like Lep-frog or MD-VV with let say , Berendsen
thermostat?
Please explain a bit.
Thanks
Tarak
On Fri, Dec 14, 2012 at 10:44 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote:
I am going to do US simulation in a protein. For this purpose I have
heated the protein from 0 to 300 K by using 'SD' integrator. But I am
bit confused with this integrator.
How good is to use Langevin Dynamics to heat a protein ?
Look at the temperature of protein and decide.
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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