AMBER Archive (2006)

Subject: AMBER: Confusion about PBC

From: anna.schrey_at_gmx.de
Date: Wed Nov 29 2006 - 10:26:04 CST

Dear amber users,

I set up an MD run as follows

 &cntrl
   imin=0, nmropt=1,
   ntx=5, irest=1,
   ntrx=1, ntpr=5000,
   ntwr=5000,
   ntwx=5000,ntwv=5000,
   ntwe=5000,
   ntf=2,ntb=1,ntc=2,
   dielc=1,cut=8,
   scnb=2,scee=1.2,
   nsnb=25, nscm=500,
   ntr=0,nstlim=25100000,
   dt=0.002,temp0=280,
   ntt=1,
   tautp=1.0,ntc=2,
  &end
 &wt type='REST',istep1=1,istep2=100000,value1=1,value2=0, &end
 &wt type='REST',istep1=100001,istep2=25100000,value1=0,value2=0, &end
 &wt type='END' &end
LISTIN=sh3_cryst_NTV_50200ps_orest.restraints
LISTOUT=sh3_cryst_NTV_50200ps_orest.violations
DISANG=sh3_cryst_all.rst

The simulation took place in a water box (WATBOX216), and the crd files contain box coordinates.

Looking at the resulting trajectory, it looked rather like a water shell than a water box, but I was sure that using ntb>1 means simulation under periodic boundary conditions. So what the reason for the strange water environment, and was I wrong to guess my simulation takes place under PBC?

Thank you very muxh,

Anna 

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