AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jul 20 2006 - 07:32:07 CDT

you can't just pick a temperature, the spacing depends on
the system size and people usually use an exponential spacing.
having said that, 10K should be enough to get exchange in
small systems, but if your is very large or in explicit solvent
then it might be too large, For those kinds of systems, though,
you really need to know what you are doing to get remd to work.

Austin B. Yongye wrote:

>>how did you determine the temperatures?
>>
>>
>Intervals of 10K, but taking tempi from the last temperature of the
>previous simulation. Is this value too wide?
>
>
>
>>it can help to run independent MD at each T
>>and make sure that the potential energy histograms
>>overlap.
>>
>>
>
>
>
>
>>Austin B. Yongye wrote:
>>
>>
>>>Dear amber users,
>>>I have been looking at the rem.log file from my replica exchange
>>>simulation (10000 exchanges, attempts every 50 steps). After the 25th
>>>step, the replicas stop exchanging energies.
>>>Is this common, or that my target temperatures are not optimal?
>>>I am running 8 replicas, with target temperatures from 300K-370K.
>>>Here is my input file:
>>>
>>>replica exchange simulation
>>> &cntrl
>>> ntwr = 50, ntwx =50, ntpr = 50, ntwprt = 385,
>>> ntt = 1, tempi = 301.9, temp0 = 340.0, tautp = 1.0,
>>> scnb = 1.0, scee = 1.0, dielc = 1, cut = 8.0,
>>> ntc = 2, ntf = 2, ntb = 2,
>>> nstlim = 50, dt = 0.001, timlim = 999999999999,
>>> ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
>>> ibelly = 0, ntr = 0, iwrap = 1,
>>> imin = 0, irest=1, ntx = 5,
>>> numexchg=10000, repcrd = 1,
>>> &end
>>>
>>>Thanks,
>>>austin-
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