On Tue, Jun 20, 2017, Ramin Salimi wrote:
>
> I am trying to pull my DNA molecule in increments of 1 A0, and then
> run equilibration for 50ps, then do another pull for 1 A0, then do the
> 50ps equilibration, and keep doing it until the molecule reaches my
> target length. My primary purpose is to keep the system in quasi-static
> condition as much as possible.
>
> So, based upon what I understood, to keep the system in quasi-static
> during both pullings, and equilibration periods, the equilibration
> periods between increments along with pulling periods should be larger
> than the relaxation time of the system.
Generally, there is no one number that qualifies as "the" relaxation time for
a system. I'm no expert on pulling simulations, but my guess is that you will
have to try different equilibration periods to examine convergence.
>
> Does it have anything to do with correlation time, and the use of IRED
> vectors, and IRED matrices in cpptraj?
No.
....dac
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Received on Tue Jun 20 2017 - 05:30:03 PDT
