[gmx-users] NVT, NPT and then pulling?

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 22:36:37 CEST 2012

On 6/27/12 4:30 PM, Steven Neumann wrote:
> Dear Gmx Users,
> I am wondering whether would you advise to run NVT, NPT (position
> restrained) and before the pulling simulation e.g of the ligand from
> protein-ligand complex? As I saw in Justin tutorial he equilibrate the
> system with only NPT ensemble before pulling. Is that really sufficent
> e.g. for 200 ps?

There is no catch-all equilibration scheme that works universally.  NVT and NPT 
are commonly run in sequence.  My systems in the tutorial are quite robust and a 
single NPT phase is sufficient.  Please do not assume that this is universally 
true.  Your protocol should be based on how stable your systems are and how well 
your desired observables converge, but that much is true of every simulation.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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