<s>
Biology	B-Algorithm
Monte	I-Algorithm
Carlo	I-Algorithm
methods	I-Algorithm
(	O
BioMOCA	O
)	O
have	O
been	O
developed	O
at	O
the	O
University	O
of	O
Illinois	O
at	O
Urbana-Champaign	O
to	O
simulate	O
ion	O
transport	O
in	O
an	O
electrolyte	O
environment	O
through	O
ion	O
channels	O
or	O
nano-pores	O
embedded	O
in	O
membranes	O
.	O
</s>
<s>
It	O
is	O
a	O
3-D	O
particle-based	O
Monte	B-Application
Carlo	I-Application
simulator	O
for	O
analyzing	O
and	O
studying	O
the	O
ion	O
transport	O
problem	O
in	O
ion	O
channel	O
systems	O
or	O
similar	O
nanopores	O
in	O
wet/biological	O
environments	O
.	O
</s>
<s>
BioMOCA	O
is	O
based	O
on	O
two	O
methodologies	O
,	O
namely	O
the	O
Boltzmann	O
transport	O
Monte	B-Application
Carlo	I-Application
(	O
BTMC	O
)	O
and	O
particle-particle-particle-mesh	O
(	O
P3M	O
)	O
.	O
</s>
<s>
The	O
first	O
one	O
uses	O
Monte	B-Algorithm
Carlo	I-Algorithm
method	I-Algorithm
to	O
solve	O
the	O
Boltzmann	O
equation	O
,	O
while	O
the	O
later	O
splits	O
the	O
electrostatic	O
forces	O
into	O
short-range	O
and	O
long-range	O
components	O
.	O
</s>
<s>
,	O
a	O
function	O
of	O
momentum	B-Algorithm
,	O
is	O
the	O
total	O
scattering	O
rate	O
for	O
all	O
collision	O
mechanisms	O
.	O
</s>
<s>
The	O
coefficients	O
ci	O
were	O
determined	O
empirically	O
for	O
a	O
1	O
M	O
KCl	O
solution	O
,	O
using	O
MD	O
simulations	O
to	O
benchmark	O
the	O
ion	O
radial	O
distribution	O
functions	O
against	O
Equilibrium	O
Monte	B-Algorithm
Carlo	I-Algorithm
simulations	I-Algorithm
.	O
</s>
<s>
Currently	O
there	O
are	O
two	O
Poisson	O
solvers	O
implemented	O
in	O
BioMOCA	O
based	O
on	O
the	O
finite	B-Algorithm
difference	I-Algorithm
method	I-Algorithm
.	O
</s>
<s>
One	O
uses	O
the	O
pre-conditioned	O
Conjugate	B-Algorithm
Gradient	I-Algorithm
scheme	I-Algorithm
(	O
pCG	O
)	O
and	O
is	O
used	O
by	O
default	O
.	O
</s>
<s>
VMD	B-Application
was	O
equipped	O
with	O
the	O
option	O
of	O
loading	O
BioMOCA	O
structures	O
.	O
</s>
<s>
Furthermore	O
,	O
BioMOCA	O
also	O
dumps	O
the	O
ion	O
trajectories	O
in	O
standard	O
formats	O
so	O
they	O
could	O
be	O
later	O
loaded	O
to	O
molecular	O
visualization	O
tools	O
such	O
as	O
VMD	B-Application
and	O
watched	O
frame	O
by	O
frame	O
in	O
a	O
movie	O
format	O
.	O
</s>
<s>
BioMOCA	O
has	O
been	O
equipped	O
with	O
the	O
option	O
of	O
dumping	O
every	O
ions	O
position	O
,	O
average	O
and	O
instantaneous	O
velocities	O
,	O
potential	O
and	O
kinetic	O
energies	O
,	O
average	O
and	O
instantaneous	O
displacements	O
and	O
other	O
info	O
at	O
every	O
step	O
(	O
or	O
few	O
steps	O
)	O
of	O
the	O
simulations	O
in	O
ASCII	B-Protocol
format	O
,	O
so	O
such	O
trajectory	O
information	O
could	O
be	O
studied	O
later	O
on	O
to	O
gather	O
further	O
statistics	O
.	O
</s>
<s>
Over	O
and	O
above	O
that	O
,	O
recoding	O
the	O
numerical	O
information	O
in	O
ASCII	B-Protocol
format	O
does	O
not	O
hold	O
its	O
machine	O
precision	O
and	O
has	O
loss	O
of	O
accuracy	O
.	O
</s>
<s>
Solving	O
such	O
problems	O
is	O
actually	O
an	O
easy	O
task	O
and	O
it	O
is	O
simply	O
to	O
avoid	O
using	O
ASCII	B-Protocol
format	O
and	O
use	O
binary	O
format	O
instead	O
.	O
</s>
