I am trying to model a surface, so need to apply periodic boundary
conditions only in x and y directions. How do I do it in AMBER 10. I am
using a non-orthogonal box as well.
My input file is
&cntrl
imin = 0, ntb = 1,
igb = 0, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 10000, dt = 0.0005,
cut = 6.0, ntr=1,
restraint_wt=100.0,
restraintmask='. 11-1300'
/
The output file just blows up. temperature and velocity shoot up like
hell..This is the equilibration step
It reads the box parameters
Box X = 45.675 Box Y = 17.948 Box Z = 38.136
Alpha = 90.000 Beta = 111.700 Gamma = 90.000
But I don't know how else to define my system. I want it to be a periodic
x-y surface and then simulate it
--
Zubin Kuvadia
PhD Candidate
Michael Doherty Research Group
Department of Chemical Engineering
University of California Santa Barbara
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Received on Fri May 25 2012 - 14:30:03 PDT
