Hi
This is my plan:
1- Pullings for 0.5 A0, then relax it for 50ps until it reaches from 40 A0 to 110 A0. Next, strip the water from the trajectories, and using GB/SA, and igb=8, run imin=5, just find the energy at different elongations. I am using GB/SA to remove the contribution of water molecules. Then plot GB/SA energy vs extension, take the derivative of the plot with respect to the extension, and get the Force vs extension plot..
The second part is called pinned simulation, and I want to pick different frames from the solvated trajectories corresponding to different lengths, strip water from them, make pdbs, and restart using Leap to do all the preparation steps; after the thermalization, and all the equilibration are done, I just run normal MD for these. And then finally try to find the entropy using the covariance matrix.
This is the source paper: Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA( by Harris, Sands, Laughton).
I don't know why I can't do this.
Ramin
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Tuesday, June 20, 2017 1:29:56 PM
To: AMBER Mailing List
Subject: Re: [AMBER] relaxation time to maintain quasi-static condition
Hi
I believe you need to dig deep into the literature before trying these
type of calculations.
What are you trying to do ?
Just pull? Pull and get good structures? pull and get free energies?
All of those things have been done by many others, so you need to go
check their papers and ask why they did what they did.
I believe your confusion has to do with your first question:
"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?"
You seems to believe that you can ONLY be at equilibrium when you pulled
zero angstroms. That is NOT correct. You are pulling, and for EACH
distance you would like to have ALL other degrees of freedom in your
system, be equilibrated. How do you do that? only ONE way: run an
infinite amount of time.
Since that is not possible, you need to come up with your own measure or
reuse someone else's.
Adrian
On 6/20/17 12:40 PM, Ramin Salimi wrote:
> 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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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 - 12:30:02 PDT
