AMBER Archive (2007)

Subject: Re: AMBER: questions about smd of amber 9

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Wed Nov 28 2007 - 16:35:10 CST

On Nov 28, 2007 4:29 PM, WANG,YING <wangying_at_ufl.edu> wrote:

> Hi, Dear all,
> I have some questions about the smd method of amber, list as
> below: Thanks very much in advance.
>
> 1. In amber, the SMD with Jarzynski relation can do the pulling
> simulation, but this method is to put a spring inside the pulling
> molecule so pull the two ends apart. If I want to fix one end and
> pull another end. How should I do in amber? frozen one c-alpha
> atom? The ibelly parameter? Could I use it with jar together?

Yes, you can fix or restrain one end.

>
>
> 2. From the mannual of amber, "One would need to repeat this
> calculation many times, starting from different snapshots from an
> equilibrium trajectory constrained at the initial distance value.
> This could be done with a long MD or a REMD simulation, and
> postprocessing with ptraj to extract snapshots." er, what's mean
> about "an equilibrium
> trajectory"?perform an energy minimisation first and then perform
> md on the stable structure? and then extract some snapshots? How
> can I know which snapshots have the same initial distance? should
> I fix the distance between these two ends and then perform an
> equlibrium simulation and then extract some snapshots?

Equilibration with smd off. Do not fix the ends. Because multiple
configurations exist for one state, you want to sample as most as you can.

>
>
> 3. As my understanding, after I get these snapshots, that is, they
> have the same distance between the two ends but with different
> atomic positions, then I perform the same smd simulation on them.
> Is it my understanding right? Yes, we can get energy average from
> some repeating simulation like that, but how about the
> force-extension relation? Different start structure should have
> different relation.......... Could I just pick up one of them? I
> think it would not be fine.

More is better. But people usually only get a few since limit of computer
resource.

>
>
> 4. And in the smd mehtod, I know that, first, let the natural
> length of the artificial spring become longer, and then, how can
> amber to figure out the position of the ends of the molecule? that
> is, how amber give the x to me? In reality, we can wait a moment
> to let the molecule acchieve a balance position. but in amber, how
> can the software to do that? also let the atoms move and then get
> the balance position? but it doesn't look like that when I do it

 Amber calculates the position of each atom. That gives you the position of
COM of group atoms you indicate in smd.

>
> .........
>
> I know that it is a long mail and too many questions, :( Sorry to
> take your time!
>
> Thanks very much!
>
> YW
>
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Hope this helps.

Wei Chen

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