Dr. Roitberg
Thanks for the response
So it follows:
1- How to figure out how far out out of equilibrium I am after pulling?? I mean is there any postprocessing method for that? But wait, doesn't it mean that I am only 0.5 A0 far from the equilibrium if I have pulled it in 0.5 A0 pulling increments?
2- During the relaxation period, as you correctly mentioned, I heard some do energy minimization during the relaxation period, and some others do equilibration. Which is that? Additionally, after each pullings, do I need to restrain the molecule to the new length with harmonic restraints during relaxation periods?
3- So you finally suggested to try different rates for both pulling, and relaxation periods. Then how to check if it is still in equilibrium or not?(I think this question partially overlaps with #1, my apologies)
Best,
Ramin
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Tuesday, June 20, 2017 7:48:05 AM
To: AMBER Mailing List
Subject: Re: [AMBER] relaxation time to maintain quasi-static condition
It might be worse tan you think.
The amount of time you need to spend during what you call
'equilibration' depends very much on how fast you pull during that
pulling part of the simulation. For example, if you pull 1 A very
slowly, then you do not need to spend much time equilibrating. If you
pull very fast, then you better spend lots of time equilibrating
(technically, relaxing).
So, it is not only the relaxation time of your system you need to worry
about, but more importantly, you need to figure out how far out of
equilibrium you are after pulling.
Unfortunately, there are no formulas or set recipes for any of this, you
need to try different ways.
adrian
On 6/20/17 8:28 AM, David Case wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jun 20 2017 - 10:00:02 PDT
