AMBER Archive (2006)

Subject: AMBER: Temperature fluctuation BIG with ntt=3

From: Mingfeng Yang (
Date: Thu Sep 21 2006 - 18:14:24 CDT

Dear Amber users,

In Amber manual, it's recommended that Langevin dynamics (ntt=3),
instead of Berendsen coupling (ntt=1), should be used to control the
temperature, especially for GB simulation. However, it seems the
temperature fluctuation (20-40) is pretty significant in the case of
ntt=3, while it's only ~6 when ntt=1.

For example, in my current system (a deca-peptide) simulated with GB
model at 300K. The temperature can sometimes jump to >400K. Is it a big

FYI, I am using Amber9/PMEMD, and my input parameters for production run
are attached (I heat the system with ntt=1 from 0K to 300K first, and
then switch to ntt=3 for production run):
   imin=0, nmropt=0,

   ntx=5, irest=1, ntrx=1,
   ntxo=1, ntpr=500, ntwr=1000, ntwprt=0, ntwx=1000, ioutfm=0,

   ntf=2, ntb=0, dielc=1.0, igb=7, saltcon=0.2,
   cut=20.0, scnb=2.0, scee=1.2,


   nstlim=2000000, temp0=300.0, tempi=300.0, nscm=50, t=0.0, dt=0.0020,

   ig=71277, ntt=3, vlimit=20.0, gamma_ln=1,

   ntp=0, pres0=1.0, comp=44.6, taup=1.0,

   ntc=2, tol=0.0001,



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