Hello Amber-onians,
I'm working on an alkane chain problem in vacuo. I set the box for
periodicity
with setBox vdw in leap and have tried various versions of periodicity
during
the equilibration but it doesn't work. What I'm seeing (vmd) are the atoms
fixed to
a certain part of the screen and then bonds becoming really long as the
alkane
chain apparantly shows up on the other side (it's aesthetic but not
scientific),
and only with ntb = 0 do I get a normal looking chain.
During equilibration, I've tried ntb = 1, ntb = 2 along with ntp =
1,
ntb = 2 along with ntp =2 and still the same affect. I've tried it with and
without
shake on so that would be ntf = 1, ntc = 1 or with ntf = 2, ntc =2, but that
didn't
change anything. During minimization I was able to use ntb = 1 and turn of
PME, but that didn't work for equilibration either.
The equilibration input file is:
Equilibration: 150 ps MD
&cntrl
imin = 0, irest = 0,
ntx = 1, ntb = 1,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 2000, dt = 0.001,
ntpr = 100, ntwx = 100, ntwr = 1000,
cut = 8, ntr=0,
ntf = 1, ntc = 1,
ibelly = 1,
bellymask = '!.SA',
&end
Is there anything I can do? What suggestions do you have?
Thanks.
--Julie
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Received on Wed Mar 16 2005 - 21:53:00 PST
