[gmx-users] Temperature in simulation

[Justin Lemkul]

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

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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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