<s>
GROMACS	B-Application
is	O
a	O
molecular	O
dynamics	O
package	O
mainly	O
designed	O
for	O
simulations	O
of	O
proteins	O
,	O
lipids	O
,	O
and	O
nucleic	O
acids	O
.	O
</s>
<s>
GROMACS	B-Application
is	O
one	O
of	O
the	O
fastest	O
and	O
most	O
popular	O
software	O
packages	O
available	O
,	O
and	O
can	O
run	O
on	O
central	B-General_Concept
processing	I-General_Concept
units	I-General_Concept
(	O
CPUs	O
)	O
and	O
graphics	B-Architecture
processing	I-Architecture
units	I-Architecture
(	O
GPUs	B-Architecture
)	O
.	O
</s>
<s>
It	O
is	O
free	O
,	O
open-source	B-Application
software	I-Application
released	O
under	O
the	O
GNU	B-License
General	I-License
Public	I-License
License	I-License
(	O
GPL	B-License
)	O
,	O
and	O
starting	O
with	O
version	O
4.6	O
,	O
the	O
GNU	B-Application
Lesser	I-Application
General	I-Application
Public	I-Application
License	I-Application
(	O
LGPL	B-Application
)	O
.	O
</s>
<s>
The	O
GROMACS	B-Application
project	O
originally	O
began	O
in	O
1991	O
at	O
Department	O
of	O
Biophysical	O
Chemistry	O
,	O
University	O
of	O
Groningen	O
,	O
Netherlands	O
(	O
1991	O
–	O
2000	O
)	O
.	O
</s>
<s>
Its	O
name	O
originally	O
derived	O
from	O
this	O
time	O
(	O
GROningen	O
MAchine	O
for	O
Chemical	O
Simulations	O
)	O
although	O
currently	O
GROMACS	B-Application
is	O
not	O
an	O
abbreviation	O
for	O
anything	O
,	O
as	O
little	O
active	O
development	O
has	O
taken	O
place	O
in	O
Groningen	O
in	O
recent	O
decades	O
.	O
</s>
<s>
The	O
molecular	O
dynamics	O
specific	O
routines	O
were	O
rewritten	O
in	O
the	O
programming	B-Language
language	I-Language
C	I-Language
from	O
the	O
Fortran	O
77-based	O
program	O
GROMOS	B-Application
,	O
which	O
had	O
been	O
developed	O
in	O
the	O
same	O
group	O
.	O
</s>
<s>
Since	O
2001	O
,	O
GROMACS	B-Application
is	O
developed	O
by	O
the	O
GROMACS	B-Application
development	O
teams	O
at	O
the	O
Royal	O
Institute	O
of	O
Technology	O
and	O
Uppsala	O
University	O
,	O
Sweden	O
.	O
</s>
<s>
GROMACS	B-Application
is	O
operated	O
via	O
the	O
command-line	B-Application
interface	I-Application
,	O
and	O
can	O
use	O
files	O
for	O
input	O
and	O
output	O
.	O
</s>
<s>
In	O
addition	O
,	O
support	O
for	O
different	O
force	O
fields	O
makes	O
GROMACS	B-Application
very	O
flexible	O
.	O
</s>
<s>
It	O
can	O
be	O
executed	O
in	O
parallel	O
,	O
using	O
Message	B-Application
Passing	I-Application
Interface	I-Application
(	O
MPI	O
)	O
or	O
threads	B-Operating_System
.	O
</s>
<s>
OpenCL	B-Application
and	O
CUDA	B-Architecture
are	O
possible	O
for	O
actual	O
GPUs	B-Architecture
of	O
AMD	O
,	O
Intel	O
,	O
and	O
Nvidia	O
with	O
great	O
acceleration	O
against	O
CPU	O
based	O
runs	O
since	O
Version	O
5	O
or	O
higher	O
.	O
</s>
<s>
In	O
Version	O
2021	O
OpenCL	B-Application
is	O
deprecated	O
and	O
SYCL	B-Language
is	O
in	O
early	O
new	O
support	O
.	O
</s>
<s>
,	O
GROMACS	B-Application
 '	O
source	O
code	O
contains	O
approximately	O
400	O
alternative	O
acronyms	O
to	O
GROMACS	B-Application
as	O
jokes	O
among	O
the	O
developers	O
and	O
biochemistry	O
researchers	O
.	O
</s>
<s>
These	O
include	O
"	O
Gromacs	B-Application
Runs	O
On	O
Most	O
of	O
All	O
Computer	O
Systems	O
"	O
,	O
"	O
Gromacs	B-Application
Runs	O
One	O
Microsecond	O
At	O
Cannonball	O
Speeds	O
"	O
,	O
"	O
Good	O
ROcking	O
Metal	O
Altar	O
for	O
Chronical	O
Sinner	O
"	O
,	O
"	O
Working	O
on	O
GRowing	O
Old	O
MAkes	O
el	O
Chrono	O
Sweat	O
"	O
,	O
and	O
"	O
Great	O
Red	O
Owns	O
Many	O
ACres	O
of	O
Sand	O
"	O
.	O
</s>
<s>
They	O
are	O
randomly	O
selected	O
to	O
possibly	O
appear	O
in	O
GROMACS	B-Application
's	O
output	O
stream	O
.	O
</s>
<s>
Under	O
a	O
non-GPL	O
license	O
,	O
GROMACS	B-Application
is	O
widely	O
used	O
in	O
the	O
Folding	B-Application
@home	I-Application
distributed	B-Architecture
computing	I-Architecture
project	O
for	O
simulations	O
of	O
protein	O
folding	O
,	O
where	O
it	O
is	O
the	O
base	O
code	O
for	O
the	O
project	O
's	O
largest	O
and	O
most	O
regularly	O
used	O
series	O
of	O
calculation	B-Application
cores	I-Application
.	O
</s>
<s>
EvoGrid	O
,	O
a	O
distributed	B-Architecture
computing	I-Architecture
project	O
to	O
evolve	O
artificial	O
life	O
,	O
also	O
employs	O
GROMACS	B-Application
.	O
</s>
