AMBER Archive (2006)

Subject: Re: AMBER: Temperature fluctuation BIG with ntt=3

From: Carlos Simmerling (
Date: Thu Sep 21 2006 - 19:48:07 CDT

you might try with sander too to see if you get similar behavior.
I think over 400K is too much change. you might also reduce step
size and see if that has any effect.

Mingfeng Yang wrote:

>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):
> &cntrl
> 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,
> ntr=0,
> 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,
> jfastw=0,
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