Many thanks to Carlos Simmerling and Guanglei Cui! Thanks.
>Dear Dr. Zhang,
>
>1. The number of MD steps between exchange attempts is controlled by
>nstlim.
>2. I'm not sure what you meant by "the last second". Instantenaous
>potential energies of the last step are used to determine if the attempt
>is accepted or not. Please refer to the original paper by Sujita, etc.
>for algorithm details.
>
>Regards,
>
>Guanglei
>
>J. Zhang, Dr wrote:
>
>> Dear Amber users,
>>
>> I am very interested in the replica exchange MD in amber 8
>> However, after reading the user guide, I can not find
>> where I can change the exchange frequency between replicas,
>> I mean after how many MD steps amber will exchange replicas.
>>
>> And another question:
>> When determining whether the exchange occurs, the potential
>> energy (E) of each replica must be known. Does amber use
>> the AVERAGE energy during the short running or the energy
>> of the last second? why?
>>
>> Thank you very much.
>>
>> Best Regards,
>>
>> ---
>> J. Zhang, Dr
>> Institute of Biophysics
>> Nanjing University
>>
>>
>>
>>
>>
>>
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Received on Mon May 31 2004 - 01:53:01 PDT
