AMBER Archive (2008)

Subject: AMBER: MD goes wrong

From: baohua zhang (
Date: Tue Sep 23 2008 - 21:17:57 CDT

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
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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