AMBER Archive (2008)

Subject: RE: AMBER: MD goes wrong

From: Ross Walker (
Date: Tue Sep 23 2008 - 23:33:43 CDT

Hi Boahua,


A few comments.


1) tempi=360.0, temp0=360.0


You are running at 360K - this is probably too hot for your protein and it
probably just unfolds.


2) nscm=50


This is very frequent to be removing center of mass translation and
rotation, are you sure you need it this often?


3) tol=0.0001


This is a VERY loose shake tolerance. Why are you changing it from the


4) heat=0.0


This option was retired way back in AMBER 8 - what version of AMBER are you


Also, what do you mean by "chaos" - how did you equilibrate your system?
What exactly happens to it. Did you equilibrate with restraints on an only
just removed the restraints? Were the energies huge during the
equilibration? - Try running 100 steps or so with ntpr=1 and ntw=1 and then
you can carefully watch the system and see how / where it blows up from. You
likely have problems with your initial structure, although the 360K probably
doesn't help.


All the best



From: [] On Behalf Of
baohua zhang
Sent: Tuesday, September 23, 2008 7:18 PM
Subject: AMBER: MD goes wrong


dear amber users:
 I am trying to run folding of my system.The problem is that when I raised
the temperature to 300K and run MD,the structure seemed to change to chaos
shortly after the begining of the simulation,while the structure remained
good after minimization and equilibrium.I just dont't know where the problem
is. here is my MD input files:
molecular dynamics

   ntx=5, irest=1, ntrx=1,
   ntxo=1, ntpr=100, ntwr=1000, ntwprt=0, ntwx=1000,

   ntf=2, ntb=2, dielc=1.0, igb=0,
   cut=9.0, scnb=2.0, scee=1.2,

   ibelly=0, ntr=0,

   nstlim=2400000, nscm=50, t=0.0, dt=0.0015,

   temp0=360.00, tempi=360.00, ig=71277, heat=0.0, ntt=1,
   tautp=1.0, vlimit=20.0,

   ntp=1, pres0=1.0, comp=44.6, taup=1.0,

   ntc=2, tol=0.0001,


 could anyone can tell me what the problem is ? thank you in advance!

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