<s>
Chemistry	B-Application
at	I-Application
Harvard	I-Application
Macromolecular	I-Application
Mechanics	I-Application
(	O
CHARMM	B-Application
)	O
is	O
the	O
name	O
of	O
a	O
widely	O
used	O
set	O
of	O
force	O
fields	O
for	O
molecular	O
dynamics	O
,	O
and	O
the	O
name	O
for	O
the	O
molecular	O
dynamics	O
simulation	O
and	O
analysis	O
computer	O
software	O
package	O
associated	O
with	O
them	O
.	O
</s>
<s>
The	O
CHARMM	B-Application
Development	O
Project	O
involves	O
a	O
worldwide	O
network	O
of	O
developers	O
working	O
with	O
Martin	O
Karplus	O
and	O
his	O
group	O
at	O
Harvard	O
to	O
develop	O
and	O
maintain	O
the	O
CHARMM	B-Application
program	O
.	O
</s>
<s>
The	O
CHARMM	B-Application
force	O
fields	O
for	O
proteins	O
include	O
:	O
united-atom	O
(	O
sometimes	O
termed	O
extended	O
atom	O
)	O
CHARMM19	B-Application
,	O
all-atom	O
CHARMM22	B-Application
and	O
its	O
dihedral	O
potential	O
corrected	O
variant	O
CHARMM22/CMAP	O
,	O
as	O
well	O
as	O
later	O
versions	O
CHARMM27	B-Application
and	O
CHARMM36	O
and	O
various	O
modifications	O
such	O
as	O
CHARMM36m	O
and	O
CHARMM36IDPSFF	O
.	O
</s>
<s>
In	O
the	O
CHARMM22	B-Application
protein	O
force	O
field	O
,	O
the	O
atomic	O
partial	O
charges	O
were	O
derived	O
from	O
quantum	O
chemical	O
calculations	O
of	O
the	O
interactions	O
between	O
model	O
compounds	O
and	O
water	O
.	O
</s>
<s>
Furthermore	O
,	O
CHARMM22	B-Application
is	O
parametrized	O
for	O
the	O
TIP3P	O
explicit	O
water	O
model	O
.	O
</s>
<s>
In	O
2006	O
,	O
a	O
special	O
version	O
of	O
CHARMM22/CMAP	O
was	O
reparametrized	O
for	O
consistent	O
use	O
with	O
implicit	O
solvent	O
GBSW	O
.	O
</s>
<s>
The	O
CHARMM22	B-Application
force	O
field	O
has	O
the	O
following	O
potential	O
energy	O
function	O
:	O
</s>
<s>
The	O
bond	O
,	O
angle	O
,	O
dihedral	O
,	O
and	O
nonbonded	O
terms	O
are	O
similar	O
to	O
those	O
found	O
in	O
other	O
force	O
fields	O
such	O
as	O
AMBER	B-Device
.	O
</s>
<s>
The	O
CHARMM	B-Application
force	O
field	O
also	O
includes	O
an	O
improper	O
term	O
accounting	O
for	O
out-of-plane	O
bending	O
(	O
which	O
applies	O
to	O
any	O
set	O
of	O
four	O
atoms	O
that	O
are	O
not	O
successively	O
bonded	O
)	O
,	O
where	O
is	O
the	O
force	O
constant	O
and	O
is	O
the	O
out-of-plane	O
angle	O
.	O
</s>
<s>
For	O
DNA	O
,	O
RNA	O
,	O
and	O
lipids	O
,	O
CHARMM27	B-Application
is	O
used	O
.	O
</s>
<s>
Some	O
force	O
fields	O
may	O
be	O
combined	O
,	O
for	O
example	O
CHARMM22	B-Application
and	O
CHARMM27	B-Application
for	O
the	O
simulation	O
of	O
protein-DNA	O
binding	O
.	O
</s>
<s>
These	O
force	O
field	O
version	O
numbers	O
refer	O
to	O
the	O
CHARMM	B-Application
version	O
where	O
they	O
first	O
appeared	O
,	O
but	O
may	O
of	O
course	O
be	O
used	O
with	O
subsequent	O
versions	O
of	O
the	O
CHARMM	B-Application
executable	O
program	O
.	O
</s>
<s>
CHARMM	B-Application
also	O
includes	O
polarizable	O
force	O
fields	O
using	O
two	O
approaches	O
.	O
</s>
<s>
The	O
CHARMM	B-Application
program	O
allows	O
for	O
generating	O
and	O
analysing	O
a	O
wide	O
range	O
of	O
molecular	O
simulations	O
.	O
</s>
<s>
More	O
advanced	O
features	O
include	O
free	O
energy	O
perturbation	O
(	O
FEP	O
)	O
,	O
quasi-harmonic	O
entropy	O
estimation	O
,	O
correlation	O
analysis	O
and	O
combined	O
quantum	O
,	O
and	O
quantum	O
mechanics	O
-	O
molecular	O
mechanics	O
(	O
QM/MM	B-Algorithm
)	O
methods	O
.	O
</s>
<s>
CHARMM	B-Application
is	O
one	O
of	O
the	O
oldest	O
programs	O
for	O
molecular	O
dynamics	O
.	O
</s>
<s>
This	O
is	O
an	O
inevitable	O
result	O
of	O
the	O
many	O
outlooks	O
and	O
groups	O
working	O
on	O
CHARMM	B-Application
worldwide	O
.	O
</s>
<s>
The	O
,	O
and	O
CHARMM	B-Application
's	O
source	O
code	O
,	O
are	O
good	O
places	O
to	O
look	O
for	O
the	O
names	O
and	O
affiliations	O
of	O
the	O
main	O
developers	O
.	O
</s>
<s>
CHARMM	B-Application
originated	O
at	O
Martin	O
Karplus	O
's	O
group	O
at	O
Harvard	O
.	O
</s>
<s>
In	O
the	O
1980s	O
,	O
finally	O
a	O
paper	O
appeared	O
and	O
CHARMM	B-Application
made	O
its	O
public	O
début	O
.	O
</s>
<s>
CHARMM	B-Application
has	O
continued	O
to	O
grow	O
and	O
the	O
latest	O
release	O
of	O
the	O
executable	O
program	O
was	O
made	O
in	O
2015	O
as	O
CHARMM40b2	O
.	O
</s>
<s>
charmm	B-Application
–	O
The	O
name	O
of	O
the	O
program	O
(	O
or	O
script	O
which	O
runs	O
the	O
program	O
)	O
on	O
the	O
computer	O
system	O
being	O
used	O
.	O
</s>
<s>
filename.inp	O
–	O
A	O
text	O
file	O
which	O
contains	O
the	O
CHARMM	B-Application
commands	O
.	O
</s>
<s>
filename.out	O
–	O
The	O
log	O
file	O
for	O
the	O
CHARMM	B-Application
run	O
,	O
containing	O
echoed	O
commands	O
,	O
and	O
various	O
amounts	O
of	O
command	O
output	O
.	O
</s>
<s>
Docking	B-Operating_System
@Home	I-Operating_System
,	O
hosted	O
by	O
University	O
of	O
Delaware	O
,	O
one	O
of	O
the	O
projects	O
which	O
use	O
an	O
open-source	B-Application
platform	I-Application
for	O
the	O
distributed	B-Architecture
computing	I-Architecture
,	O
BOINC	B-Operating_System
,	O
used	O
CHARMM	B-Application
to	O
analyze	O
the	O
atomic	O
details	O
of	O
protein-ligand	O
interactions	O
in	O
terms	O
of	O
molecular	O
dynamics	O
(	O
MD	O
)	O
simulations	O
and	O
minimizations	O
.	O
</s>
<s>
World	B-Operating_System
Community	I-Operating_System
Grid	I-Operating_System
,	O
sponsored	O
by	O
IBM	O
,	O
ran	O
a	O
project	O
named	O
The	O
Clean	O
Energy	O
Project	O
which	O
also	O
used	O
CHARMM	B-Application
in	O
its	O
first	O
phase	O
which	O
has	O
completed	O
.	O
</s>
