Re: AMBER: questions about smd of amber 9

From: WANG,YING <>
Date: Wed, 28 Nov 2007 21:14:21 -0500 (EST)

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

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!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 02 2007 - 06:07:14 PST
Custom Search