On 10/3/12 2:02 PM, Shima Arasteh wrote:
You are right and I will insert the native protein in membrane. To do so, I
want to set the temperature of nvt.mdp file to 300 K, however I want to use the
result output of memrane simulated in 310 K for 50 ns.
Through your earlier suggestions, I got that velocities would be reassigned in
new simulation and 10 degree is not a thing to be concerned in my system.
Here, I'd like to know if I am criticized for using this difference between
temperatures?
It would be preferable to equilibrate the membrane at the desired temperature
before perturbing it with the introduction of a protein. I would assume that
any effect on the dynamics would be minimal, but assumptions don't get you past
a critical audience. It can't hurt to run a short equilibration (10-20 ns
maybe) of the membrane at 300 K before introducing the peptide. It's more
intuitive and should not take very long to do.
-Justin
--
========================================
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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