<s>
Assisted	O
Model	O
Building	O
with	O
Energy	O
Refinement	O
(	O
AMBER	B-Application
)	O
is	O
a	O
family	O
of	O
force	O
fields	O
for	O
molecular	O
dynamics	O
of	O
biomolecules	O
originally	O
developed	O
by	O
Peter	O
Kollman	O
's	O
group	O
at	O
the	O
University	O
of	O
California	O
,	O
San	O
Francisco	O
.	O
</s>
<s>
AMBER	B-Application
is	O
also	O
the	O
name	O
for	O
the	O
molecular	O
dynamics	O
software	B-Application
package	I-Application
that	O
simulates	O
these	O
force	O
fields	O
.	O
</s>
<s>
The	O
term	O
AMBER	B-Application
force	O
field	O
generally	O
refers	O
to	O
the	O
functional	O
form	O
used	O
by	O
the	O
family	O
of	O
AMBER	B-Application
force	O
fields	O
.	O
</s>
<s>
This	O
form	O
includes	O
several	O
parameters	O
;	O
each	O
member	O
of	O
the	O
family	O
of	O
AMBER	B-Application
force	O
fields	O
provides	O
values	O
for	O
these	O
parameters	O
and	O
has	O
its	O
own	O
name	O
.	O
</s>
<s>
To	O
use	O
the	O
AMBER	B-Application
force	O
field	O
,	O
it	O
is	O
necessary	O
to	O
have	O
values	O
for	O
the	O
parameters	O
of	O
the	O
force	O
field	O
(	O
e.g.	O
</s>
<s>
A	O
fairly	O
large	O
number	O
of	O
these	O
parameter	O
sets	O
exist	O
,	O
and	O
are	O
described	O
in	O
detail	O
in	O
the	O
AMBER	B-Application
software	O
user	O
manual	O
.	O
</s>
<s>
As	O
of	O
2018	O
the	O
primary	O
protein	O
model	O
used	O
by	O
the	O
AMBER	B-Application
suit	O
is	O
the	O
ff14SB	O
force	O
field	O
.	O
</s>
<s>
General	O
AMBER	B-Application
force	O
field	O
(	O
GAFF	O
)	O
provides	O
parameters	O
for	O
small	O
organic	O
molecules	O
to	O
facilitate	O
simulations	O
of	O
drugs	O
and	O
small	O
molecule	O
ligands	O
in	O
conjunction	O
with	O
biomolecules	O
.	O
</s>
<s>
The	O
primary	O
force	O
field	O
used	O
in	O
the	O
AMBER	B-Application
suit	O
for	O
lipids	O
is	O
lipid14	O
.	O
</s>
<s>
The	O
AMBER	B-Application
software	O
suite	O
provides	O
a	O
set	O
of	O
programs	O
to	O
apply	O
the	O
AMBER	B-Application
forcefields	O
to	O
simulations	O
of	O
biomolecules	O
.	O
</s>
<s>
It	O
is	O
written	O
in	O
the	O
programming	O
languages	O
Fortran	B-Application
90	O
and	O
C	B-Language
,	O
with	O
support	O
for	O
most	O
major	O
Unix-like	B-Operating_System
operating	I-Operating_System
systems	I-Operating_System
and	O
compilers	B-Language
.	O
</s>
<s>
New	O
versions	O
are	O
released	O
usually	O
in	O
the	O
spring	O
of	O
even	O
numbered	O
years	O
;	O
AMBER	B-Application
10	O
was	O
released	O
in	O
April	O
2008	O
.	O
</s>
<s>
The	O
software	O
is	O
available	O
under	O
a	O
site	B-License
license	I-License
agreement	O
,	O
which	O
includes	O
full	O
source	O
,	O
currently	O
priced	O
at	O
US$500	O
for	O
non-commercial	O
and	O
US$	O
20,000	O
for	O
commercial	O
organizations	O
.	O
</s>
<s>
It	O
was	O
designed	O
for	O
parallel	B-Operating_System
computing	I-Operating_System
,	O
and	O
performs	O
significantly	O
better	O
than	O
SANDER	O
when	O
running	O
on	O
more	O
than	O
8	O
–	O
16	O
processors	O
.	O
</s>
<s>
pmemd.cuda	O
runs	O
simulations	O
on	O
machines	O
with	O
graphics	B-Architecture
processing	I-Architecture
units	I-Architecture
(	O
GPUs	B-Architecture
)	O
.	O
</s>
<s>
AMBER	B-Application
includes	O
no	O
visualizing	O
abilities	O
,	O
which	O
is	O
commonly	O
performed	O
with	O
Visual	B-Application
Molecular	I-Application
Dynamics	I-Application
(	O
VMD	O
)	O
.	O
</s>
<s>
cpptraj	O
is	O
a	O
rewritten	O
version	O
of	O
ptraj	O
made	O
in	O
C++	B-Language
to	O
give	O
faster	O
analysis	O
of	O
simulation	O
results	O
.	O
</s>
