> On Apr 5, 2017, at 6:05 PM, pengfei li <ldsoar1990.gmail.com> wrote:
>
> Hi Jason,
>
> Thanks for the answer. Since degrees of freedom will also be counted for restrained atoms, in the equilibration procedure intended to equilibrated the solvents only, will performing Langevin dynamics with a very strong restraint on protein atoms (e.g. 500 kcal/(mol*A^2)) towards the initial configuration cause any danger?
Yes, but for a different reason. Force constants this strong result in very high frequency motions that require a short time step to integrate with acceptable accuracy.
This is stronger than force constants involving hydrogen atoms and heavy atoms which are usually constrained to allow us to take 2 fs timesteps instead of 1 fs.
Remember that restrained atoms can still have a sizeable velocity, but they will never wander far from the reference positions. So they will still contribute kinetic energy to the system as a whole. Constrained degrees of freedom by definition contribute 0 (which is why they are excluded).
> Like the protein atoms are strongly restrained (hence very small velocities)
Careful. Strong restraints does NOT mean small velocities. It just means motion on average oscillates closely around a fixed reference.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 05 2017 - 15:30:04 PDT
