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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Received on Sun Dec 03 2006 - 06:07:12 PST
