Re: AMBER: MD goes wrong

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 23 Sep 2008 23:19:19 -0400

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 adrian.qtp.ufl.edu
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Received on Wed Sep 24 2008 - 05:11:36 PDT