AMBER Archive (2008)

Subject: Re: AMBER: MD goes wrong

From: Adrian Roitberg (
Date: Tue Sep 23 2008 - 22:19:19 CDT

I do not know what 'change to
chaos' means, but the input you sent is running at 360 degrees as
indicated by:

> temp0=360.00, tempi=360.00

So, what do you mean exactly ?

baohua zhang wrote:
> 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
> chaosshortly 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
> &cntrl
> imin=0,
> 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,
> ipol=0,
> 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,
> jfastw=0,
> &end
> could anyone can tell me what the problem is ? thank you in advance!

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

Senior Editor. Journal of Physical Chemistry American Chemical Society

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to