QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: run on April 3, 2012, 12:29

Title: Is it reasonable for this statement
Post by: run on April 3, 2012, 12:29

If I execute molecular simulation according following script. We describe the method as ‘we execute an dynamics simulation on the system at room temperature (T=300 K) with a time step of 1 fs.’ Is it reasonable for this statement? If it is not reasonable.  How should I describe this method in right way.

initial_velocity = MaxwellBoltzmannDistribution(
        temperature=300.0*Kelvin
    )
method = VelocityVerlet(
        time_step=1.0*femtoSecond,
        initial_velocity=initial_velocity
    )

Title: Re: Is it reasonable for this statement
Post by: kstokbro on April 3, 2012, 14:48

Suggestion
We perform a molecular dynamics simulation of the system with an initial velocity distribution according to at room temperature of  (T=300K) and using a time step of 1 fs.

 Note that after a few time steps, you might not have a room temperature distribution any more.  To have a room temperature distribution you need to equilibrate you system, using forinstance the NVTBerendsen method or reset you velocity distribution several times in the md,
see
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.nvtberendsen.html

Title: Re: Is it reasonable for this statement
Post by: run on April 5, 2012, 05:22

Thanks!