Author Topic: Is it reasonable for this statement  (Read 3253 times)

0 Members and 1 Guest are viewing this topic.

Offline run

  • Regular QuantumATK user
  • **
  • Posts: 7
  • Reputation: 0
    • View Profile
Is it reasonable for this statement
« 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
    )
« Last Edit: April 3, 2012, 13:56 by run »

Offline kstokbro

  • Supreme QuantumATK Wizard
  • *****
  • Posts: 392
  • Reputation: 13
    • View Profile
    • QuantumWise
Re: Is it reasonable for this statement
« Reply #1 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

Offline run

  • Regular QuantumATK user
  • **
  • Posts: 7
  • Reputation: 0
    • View Profile
Re: Is it reasonable for this statement
« Reply #2 on: April 5, 2012, 05:22 »
Thanks!