AMBER Archive (2008)

Subject: AMBER: Temperature regulation

From: julliane Yoneda (
Date: Mon Sep 15 2008 - 19:48:50 CDT

Dear AMBER users,
I am running a restrained molecular dynamics simulation in vacuum with the following input:
imin = 0, irest= 1, ntpr= 50, ntf=2,
ntwx =100, ntb = 0, ntx = 5, ntc = 2, nsnb=10,
nstlim = 100000, cut = 9.0, igb = 0, ntr=1,
t = 30.0, dt =0.002,
tempi = 300.0, temp0 = 300.0, ntt = 1, dtemp=4.,
I divided the simulation in 10 parts using the same input. Everything seems to be ok in the output.
The problem is that every time the simulation is restarted the temperature oscillates to 240 K… I tried to use ntt=4 but is seems to be worst because the temperature goes to 150K… I don’t understand what is happening…
Could someone help me, please?
Thank you very much;
                                                 Julliane Yoneda
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