Re: AMBER: Replica exchange

From: Guanglei Cui <cuigl.csb.sunysb.edu>
Date: Wed, 19 Jul 2006 14:24:55 -0400

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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Received on Sun Jul 23 2006 - 06:07:04 PDT
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