Thanks for the responses.
austin-
> also note that REMD in amber requires that inpcrd files
> have velocities, so you have to run MD for at least a
> few steps to get velocities. You can do that for each replica or use
> a single restart file with velocities as inpcrd for all replicas.
>
> Guanglei Cui wrote:
>
>> Hi Austin,
>>
>> I think it's better to have the replicas separately equilibrated to
>> their target temperatures before you commit them to the exchange. Is
>> there any particular reason that you want to cold start all of them
>> other than convenience?
>>
>> Guanglei
>>
>> Austin B. Yongye wrote:
>>
>>> Dear amber users,
>>> I am running some replica exchange simulations and split between two
>>> options:
>>>
>>> Is it better to
>>> 1. Equilibrate a single structure in a solvent to a particular
>>> temperature
>>> eg 300K and then generate the replicas from this point with different
>>> target temperatures, irest=1, ntx=5, etc?
>>>
>>> 2. Start with all the replicas at 0K and give each replica a different
>>> target temperature, irest=0, ntx=1, etc?
>>>
>>> Thanks,
>>> austin-
>>>
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Received on Wed Jul 19 2006 - 06:07:08 PDT
