AMBER Archive (2007)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Nov 29 2007 - 10:56:15 CST

Just to be clear.

Gustavo Seabra got the answers right, because there is a trick to things.

"So you need to run many times smd from different starting
point." DOES not mean different distances, it means different snapshots
BELONGING to the ensemble restrained at the initial distance.

Adrian

Wei Chen wrote:
> 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
> point.
>
> Wei
>
> On Nov 28, 2007 9:14 PM, WANG,YING <wangying_at_ufl.edu> 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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> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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