AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jul 19 2006 - 13:24:55 CDT

Hi,

In addition to Carlos's question, I notice that you have a nstlim of 50
steps. That's awfully short. In your input, you have scnb and scee both
altered from the default value. I'm not sure that's recommended to do.

Guanglei

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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