Re: AMBER: questions about smd of amber 9

From: Wei Chen <>
Date: Thu, 29 Nov 2007 11:28:34 -0500

Yes, you run equilibration before smd. You should pick snapshots when the
system is already in equilibrium. Properties like free energy are actually
ensemble averages. So you need to run many times smd from different starting


On Nov 28, 2007 9:14 PM, WANG,YING <> wrote:

> Thanks very much!!
> I still have some questions, as below:
> >> 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.
> Could you explain little bit more about Equilibration with smd
> off?
> You means just run md after the energy minimisation and without
> set jar parameters? But how can I know which configurations are
> that I expect to get? This process should be done before smd and
> then use the different configurations to do smd, is it right?
> Thanks very much for your answer!! It really help me a lot!
> YW
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Received on Sun Dec 02 2007 - 06:07:21 PST
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