DNA dissociation in Ewald simulation

From: Michael Cooney <mike_at_bmbiris.bmb.uga.edu>
Date: Fri 17 Nov 2000 16:39:05 -0500 (EST)

Dear Amber users,

I am running a molecular dynamics simulation on a protein:DNA
complex in a water box using PME and periodic boundary conditions,
but with sander_classic rather than the new sander. After ~10 ps
of production MD at 300K (the system was first ramped up from
5K->300K with nmropt), the solute migrates toward the edge of the box
and the DNA strands dissociate from each other, eventually ending up
more than 40A apart.
This may be an imaging problem, but I would very much appreciate any
suggestions. Here is my input file, and I can send an output PDB file
as an attachment if necessary.

# unrestrained dynamics: heating 50 ps, 5K to 300K
    imin=0, nmropt=1, iewald=1,
    irest=1, init=4, ntx=7, isolvp=1507,
    ntpr=500, ntwx=25, ntwe=25,
    ntf=2, idiel=1, dielc=1.0, cut=8.0,
    nsnb=10, scnb=2.0, scee=1.2,
    nrun=100, nstlim=500, dt=0.002
    temp0=300.0, tempi=300.0, ntt=5, tautp=0.25, tauts=0.25,
    taup=0.2, ntc=2, ntb=2, ntp=2,
48.562787 45.586608 68.869403 90.0 90.0 90.0
48.562787 45.586608 68.869403 4.0 0.0 0.0 0.0
   type='TEMP0', istep1=0, istep2=50000,
                 value1=300.0, value2=300.0,


Thank you in advance for your help.

Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
Received on Fri Nov 17 2000 - 13:39:05 PST
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