<s>
Desmond	B-Application
is	O
a	O
software	O
package	O
developed	O
at	O
D	B-Application
.	I-Application
E	I-Application
.	I-Application
Shaw	I-Application
Research	I-Application
to	O
perform	O
high-speed	O
molecular	O
dynamics	O
simulations	O
of	O
biological	O
systems	O
on	O
conventional	O
computer	B-Architecture
clusters	I-Architecture
.	O
</s>
<s>
The	O
core	O
and	O
source	O
code	O
are	O
available	O
at	O
no	O
cost	O
for	O
non-commercial	O
use	O
by	O
universities	O
and	O
other	O
not-for-profit	O
research	O
institutions	O
,	O
and	O
have	O
been	O
used	O
in	O
the	O
Folding	B-Application
@home	I-Application
distributed	O
computing	O
project	O
.	O
</s>
<s>
Desmond	B-Application
is	O
available	O
as	O
commercial	B-Application
software	I-Application
through	O
Schrödinger	O
,	O
Inc	O
.	O
</s>
<s>
Desmond	B-Application
supports	O
algorithms	O
typically	O
used	O
to	O
perform	O
fast	O
and	O
accurate	O
molecular	O
dynamics	O
.	O
</s>
<s>
Desmond	B-Application
can	O
compute	O
energies	O
and	O
forces	O
for	O
many	O
standard	O
fixed-charged	O
force	O
fields	O
used	O
in	O
biomolecular	O
simulations	O
,	O
and	O
is	O
also	O
compatible	O
with	O
polarizable	O
force	O
fields	O
based	O
on	O
the	O
Drude	O
formalism	O
.	O
</s>
<s>
A	O
variety	O
of	O
integrators	O
and	O
support	O
for	O
various	O
ensembles	O
have	O
been	O
implemented	O
in	O
the	O
code	O
,	O
including	O
methods	O
for	O
temperature	O
control	O
(	O
Andersen	O
,	O
Nosé-Hoover	B-Algorithm
,	O
and	O
Langevin	O
)	O
and	O
pressure	O
control	O
(	O
Berendsen	B-Algorithm
,	O
Martyna-Tobias-Klein	O
,	O
and	O
Langevin	O
)	O
.	O
</s>
<s>
Desmond	B-Application
can	O
also	O
be	O
used	O
to	O
perform	O
absolute	O
and	O
relative	O
free	O
energy	O
calculations	O
(	O
e.g.	O
,	O
free	O
energy	O
perturbation	O
)	O
.	O
</s>
<s>
Other	O
simulation	O
methods	O
(	O
such	O
as	O
replica	B-Algorithm
exchange	I-Algorithm
)	O
are	O
supported	O
through	O
a	O
plug-in-based	O
infrastructure	O
,	O
which	O
also	O
allows	O
users	O
to	O
develop	O
their	O
own	O
simulation	O
algorithms	O
and	O
models	O
.	O
</s>
<s>
Desmond	B-Application
is	O
also	O
available	O
in	O
a	O
graphics	B-Architecture
processing	I-Architecture
unit	I-Architecture
(	O
GPU	B-Architecture
)	O
accelerated	O
version	O
that	O
is	O
about	O
60-80	O
times	O
faster	O
than	O
the	O
central	B-General_Concept
processing	I-General_Concept
unit	I-General_Concept
(	O
CPU	O
)	O
version	O
.	O
</s>
<s>
Along	O
with	O
the	O
molecular	O
dynamics	O
program	O
,	O
the	O
Desmond	B-Application
software	O
also	O
includes	O
tools	O
for	O
minimizing	O
and	O
energy	O
analysis	O
,	O
both	O
of	O
which	O
can	O
be	O
run	O
efficiently	O
in	O
a	O
parallel	O
environment	O
.	O
</s>
<s>
It	O
currently	O
supports	O
several	O
versions	O
of	O
the	O
CHARMM	O
,	O
Amber	O
and	O
OPLS	B-Algorithm
force	O
fields	O
,	O
and	O
a	O
range	O
of	O
different	O
water	O
models	O
.	O
</s>
<s>
Desmond	B-Application
is	O
integrated	O
with	O
a	O
molecular	O
modeling	O
environment	O
(	O
Maestro	O
,	O
developed	O
by	O
Schrödinger	O
,	O
Inc	O
.	O
)	O
for	O
setting	O
up	O
simulations	O
of	O
biological	O
and	O
chemical	O
systems	O
,	O
and	O
is	O
compatible	O
with	O
Visual	B-Application
Molecular	I-Application
Dynamics	I-Application
(	O
VMD	O
)	O
for	O
trajectory	O
viewing	O
and	O
analysis	O
.	O
</s>
