AMBER Archive (2007)

Subject: AMBER: questions about smd of amber 9

From: WANG,YING (wangying_at_ufl.edu)
Date: Wed Nov 28 2007 - 15:29:41 CST

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?

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?

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.

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
.........

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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