<s>
Name	O
View	B-Device
3D	I-Device
Model	O
builder	O
Min	O
MD	O
MC	O
REM	O
QM	O
Imp	O
GPU	B-Architecture
Comments	O
License	B-License
Website	O
ACEMDHigh	O
Performance	O
molecular	O
dynamic	O
simulation	O
softwareProprietary	O
,	O
Free	O
for	O
1	O
GPUACEMD	O
AMBERHigh	O
Performance	O
MD	O
,	O
Comprehensive	O
analysis	O
toolsProprietary	O
,	O
Free	O
open	O
sourceAMBER	O
MD	O
Abalone	B-Application
Biomolecular	O
simulations	O
,	O
protein	O
folding	O
.	O
</s>
<s>
,	O
gratis	O
,	O
commercial	B-Application
Agile	O
Molecule	O
ADF	B-Application
Modeling	O
suite	O
:	O
ReaxFF	B-Algorithm
,	O
UFF	O
,	O
QM-MM	O
with	O
Amber	B-Device
and	O
Tripos	O
force	O
fields	O
,	O
DFT	O
and	O
semi-empirical	O
methods	O
,	O
conformational	O
analysis	O
with	O
RDKit	O
;	O
partly	O
GPU-accelerated	O
,	O
commercial	B-Application
,	O
gratis	O
trial	O
SCM	O
Ascalaph	B-Application
Designer	I-Application
Molecular	O
building	O
(	O
DNA	O
,	O
proteins	O
,	O
hydrocarbons	O
,	O
nanotubes	O
)	O
,	O
molecular	O
dynamics	O
,	O
GPU	B-Architecture
acceleration	O
Ascalaph	O
Project	O
Avogadro	B-Language
Molecule	O
building	O
,	O
editing	O
(	O
peptides	O
,	O
small	O
molecules	O
,	O
crystals	O
)	O
,	O
conformational	O
analysis	O
,	O
2D/3D	O
conversion	O
;	O
extensible	O
interfaces	O
to	O
other	O
tools	O
open	B-Application
source	I-Application
GNU	B-License
GPL	I-License
Avogadro	B-Language
BOSS	B-Application
OPLS	B-Algorithm
Yale	O
University	O
CHARMM	B-Application
Commercial	B-Application
version	O
with	O
multiple	O
graphical	O
front	O
ends	O
is	O
sold	O
by	O
BIOVIA	O
(	O
as	O
CHARMm	B-Application
)	O
,	O
formerly	O
Accelrys	O
.	O
</s>
<s>
,	O
commercial	B-Application
charmm.org	O
CHEMKIN	B-Application
Chemical	O
reaction	O
kinetics	O
.	O
</s>
<s>
CHEMKIN	B-Application
CP2K	B-Application
CP2K	B-Application
can	O
perform	O
atomistic	O
and	O
molecular	O
simulations	O
of	O
solid	O
state	O
,	O
liquid	O
and	O
biological	O
systems	O
.	O
</s>
<s>
open	B-Application
source	I-Application
GNU	O
GPLv2	O
or	O
later	O
CP2K	B-Application
Desmond	B-Application
High	B-Architecture
performance	I-Architecture
MD	O
;	O
has	O
comprehensive	O
GUI	O
to	O
build	O
,	O
visualize	O
,	O
and	O
review	O
results	O
and	O
calculation	O
setup	O
up	O
and	O
launch	O
,	O
commercial	B-Application
or	O
gratis	O
D	O
.	O
E	O
.	O
Shaw	O
Research	O
Schrödinger	O
Discovery	B-Application
Studio	I-Application
Comprehensive	O
life	O
science	O
modeling	O
and	O
simulation	O
suite	O
of	O
applications	O
focused	O
on	O
optimizing	O
drug	O
discovery	O
process	O
:	O
small	O
molecule	O
simulations	O
,	O
QM-MM	O
,	O
pharmacophore	O
modeling	O
,	O
QSAR	O
,	O
protein-ligand	O
docking	O
,	O
protein	O
homology	O
modeling	O
,	O
sequence	O
analysis	O
,	O
protein-protein	O
docking	O
,	O
antibody	O
modeling	O
,	O
etc	O
.	O
</s>
<s>
,	O
trial	O
available	O
Dassault	O
Systèmes	O
BIOVIA(formerly Accelrys )	O
fold.it	B-Language
Y	O
/	O
I	O
University	O
of	O
Washington	O
and	O
The	O
Baker	O
Labs	O
;	O
structure	O
prediction	O
,	O
protein	O
folding	O
,	O
commercial	B-Application
or	O
gratis	O
fold.it	B-Language
download	O
page	O
FoldX	B-Application
Energy	O
calculations	O
,	O
protein	O
design	O
,	O
commercial	B-Application
or	O
gratis	O
CRG	O
GROMACS	B-Application
Implicit	O
Solvent	O
–	O
Gromacs	B-Application
High	B-Architecture
performance	I-Architecture
MD	O
open	B-Application
source	I-Application
GNU	B-License
GPL	I-License
gromacs.org	O
GROMOS	B-Application
Intended	O
for	O
biomolecules	O
,	O
commercial	B-Application
GROMOS	B-Application
website	O
LAMMPS	B-Application
Has	O
potentials	O
for	O
soft	O
and	O
solid-state	O
materials	O
and	O
coarse-grain	O
systems	O
open	B-Application
source	I-Application
,	O
GNU	O
GPLv2	O
Sandia	O
MacroModel	B-Application
OPLS-AA	O
,	O
MMFF	O
,	O
GBSA	O
solvent	O
model	O
,	O
conformational	O
sampling	O
,	O
minimizing	O
,	O
MD	O
.	O
</s>
<s>
Schrödinger	O
MAPS	O
Building	O
,	O
visualizing	O
,	O
and	O
analysis	O
tools	O
in	O
one	O
user	O
interface	O
,	O
with	O
access	O
to	O
multiple	O
simulation	O
engines	O
,	O
trial	O
available	O
Scienomics	O
Materials	B-Application
Studio	I-Application
Environment	O
that	O
brings	O
materials	O
simulation	O
technology	O
to	O
desktop	O
computing	O
,	O
solving	O
key	O
problems	O
in	O
R&D	O
processes	O
,	O
trial	O
available	O
Dassault	O
Systèmes	O
BIOVIA(formerly Accelrys )	O
MBN	B-Application
Explorer	I-Application
+	O
MBN	O
Studio	O
Standard	O
and	O
reactive	O
CHARMM	B-Application
force	O
fields	O
;	O
molecular	O
modeler	O
(	O
carbon	O
nanomaterials	O
,	O
biomolecules	O
,	O
nanocrystals	O
)	O
;	O
explicit	O
library	O
of	O
examples	O
,	O
free	O
trial	O
available	O
MBN	O
Research	O
Center	O
MDynaMix	B-Language
Parallel	O
MD	O
open	B-Application
source	I-Application
GNU	B-License
GPL	I-License
Stockholm	O
University	O
MOE	B-Application
Molecular	B-Application
Operating	I-Application
Environment	I-Application
(	O
MOE	B-Application
)	O
Chemical	O
Computing	O
Group	O
ms2	B-Algorithm
direct	O
on	O
the	O
fly	O
computation	O
of	O
large	O
number	O
of	O
thermophysical	O
properties	O
.	O
</s>
<s>
Main	O
application	O
of	O
ms2	B-Algorithm
is	O
on	O
fluids	O
.	O
</s>
<s>
open	O
sourcems-2.de	O
Orac	B-Application
Molecular	O
dynamics	O
simulation	O
program	O
to	O
explore	O
free	O
energy	O
surfaces	O
in	O
biomolecular	O
systems	O
at	O
the	O
atomic	O
level	O
open	B-Application
source	I-Application
Orac	B-Application
download	O
page	O
NAMD	B-Application
+	O
VMD	B-Application
Fast	O
,	O
parallel	O
MD	O
,	O
CUDA	B-Architecture
,	O
free	O
academic	O
use	O
,	O
source	O
code	O
Beckman	O
Institute	O
NWChem	B-Application
High-performance	O
computational	O
chemistry	O
software	O
,	O
includes	O
quantum	O
mechanics	O
,	O
molecular	O
dynamics	O
and	O
combined	O
QM-MM	O
methods	O
open	B-Application
source	I-Application
,	O
Educational	O
Community	O
License	B-License
version	O
2.0	O
NWChem	B-Application
Protein	B-Algorithm
Local	I-Algorithm
Optimization	I-Algorithm
Program	I-Algorithm
Helix	O
,	O
loop	O
,	O
and	O
side	O
chain	O
optimizing	O
,	O
fast	O
energy	O
minimizing	O
PLOP	O
wiki	O
Q	B-Application
(	O
I	O
)	O
Free	O
energy	O
perturbation	O
(	O
FEP	O
)	O
simulations	O
,	O
(	O
II	O
)	O
empirical	O
valence	O
bond	O
(	O
EVB	O
)	O
,	O
calculations	O
of	O
reaction	O
free	O
energies	O
,	O
(	O
III	O
)	O
linear	O
interaction	O
energy	O
(	O
LIE	O
)	O
calculations	O
of	O
receptor-ligand	O
binding	O
affinities	O
open	B-Application
source	I-Application
GNU	O
GPLv2	O
or	O
later	O
Q	B-Application
QuantumATK	O
Complete	O
atomistic	O
modeling	O
platform	O
for	O
material	O
science	O
.	O
</s>
<s>
,	O
commercial	B-Application
Synopsys	O
QuantumATK	O
SAMSON	B-Application
Computational	O
nanoscience	O
(	O
life	O
sciences	O
,	O
materials	O
,	O
etc	O
.	O
)	O
.	O
</s>
<s>
Modular	O
architecture	O
,	O
modules	O
termed	O
SAMSON	B-Application
Elements	O
,	O
gratis	O
SAMSON	B-Application
Connect	O
Scigress	B-Application
MM	O
,	O
DFT	O
,	O
semiempirical	O
methods	O
,	O
parallel	O
MD	O
,	O
conformational	O
analysis	O
,	O
Linear	O
scaling	O
SCF	O
,	O
docking	O
protein-ligand	O
,	O
Batch	B-General_Concept
processing	I-General_Concept
,	O
virtual	O
screening	O
,	O
automated	O
builders	O
(	O
molecular	O
dynamics	O
,	O
proteins	O
,	O
crystals	O
)	O
SCIGRESS.com	O
Spartan	B-Application
Small	O
molecule	O
(	O
<	O
2,000	O
a.m.u.	O
)	O
</s>
<s>
,	O
free	O
trial	O
available	O
Wavefunction	O
,	O
Inc	O
.	O
TeraChem	O
High	B-Architecture
performance	I-Architecture
GPU-accelerated	O
ab	O
initio	O
molecular	O
dynamics	O
and	O
TD/DFT	O
software	O
package	O
for	O
very	O
large	O
molecular	O
or	O
even	O
nanoscale	O
systems	O
.	O
</s>
<s>
Runs	O
on	O
NVIDIA	O
GPUs	B-Architecture
and	O
64-bit	B-Device
Linux	B-Application
,	O
has	O
heavily	O
optimized	O
CUDA	B-Architecture
code	O
.	O
</s>
<s>
Software	O
tools	O
for	O
molecular	O
design-Tinker-HP	O
,	O
gratis	O
Washington	O
University	O
UCSF	B-Application
Chimera	I-Application
Visually	O
appealing	O
viewer	O
,	O
amino	O
acid	O
rotamers	O
and	O
other	O
building	O
,	O
includes	O
Antechamber	O
and	O
MMTK	O
,	O
Ambertools	O
plugins	O
in	O
development	O
.	O
</s>
