AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Wed Jul 19 2006 - 12:23:47 CDT

> 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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>
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