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Removed gmx dyndom
2018-12-04
David van der Spoel
R
e
moved gm
x
dy
n
dom
commit
|
commitdiff
|
tree
2018-12-04
Da
v
id van der Spoel
Removed
gm
x
anado
c
k
commit
|
commitdiff
|
tree
2018-11-21
Dav
i
d va
n
d
er Spoel
Merge bran
c
h '
r
elease-2019'
commit
|
commitdiff
|
tree
2018-11-18
Davi
d
van
d
er
S
p
o
el
A
d
d
e
d
citation for new analy
s
is
function
a
lity
.
commit
|
commitdiff
|
tree
2018-11-11
D
a
v
id v
a
n der S
p
oel
Fix entropy cal
c
ulati
o
n in
g
mx an
a
eig
commit
|
commitdiff
|
tree
2018-11-09
D
avid van der
Sp
o
el
Change g
e
t_atom_
i
ndex to allow multip
l
e molecul
e
s
.
commit
|
commitdiff
|
tree
2018-10-11
D
a
vid van der Spoe
l
Reinstated quasiharmo
n
ic entropy
c
alculation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David
v
an de
r
Sp
o
el
Added option to gm
x
nmeig t
o
prin
t
ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
David van der Spoe
l
Le
t
gmx nmeig
p
r
i
nt th
e
r
m
ochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
D
avid van
d
er Spoel
Renamed ent
r
opy
.
* to t
h
ermochemis
t
ry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der
Spoel
Split off
entropy calculation to
s
e
parate file
.
commit
|
commitdiff
|
tree
2017-12-28
David van de
r
Spoel
Fixes and updates for xplor2gml
.
p
l
a
nd ato
m
_nom
.
t
b
l
commit
|
commitdiff
|
tree
2017-11-06
David v
a
n der
Spoel
Fixed check for wa
t
er in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
D
a
v
i
d
van de
r
S
p
oel
New mdp input
f
or
e
lectric f
i
elds
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
F
ixed mdp
o
u
tput
f
rom electric
field
code
.
commit
|
commitdiff
|
tree
2017-10-30
Davi
d
van der Spoel
A
d
ded o
p
tio
n
-wate
r
ti
p
s
3p
to pdb2
g
mx
.
commit
|
commitdiff
|
tree
2017-10-23
David van
der Spo
e
l
Split off th
e
NMR re
l
ated analyses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
avid van der Spoel
Fixed
miss
i
ng
ent
r
ies
i
n nrnb
a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-15
David
v
an der Spoel
Work
e
d around
m
issi
n
g OpenMP implementa
t
ion in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David
va
n
der
S
poel
Fixed bug in
g
mx disres ind
e
x
i
ng array
s
.
commit
|
commitdiff
|
tree
2017-08-02
Davi
d
van der S
p
oe
l
Worked aro
u
nd missing OpenMP impleme
n
tatio
n
in o
r
ires
.
commit
|
commitdiff
|
tree
2017-07-28
David van
d
er Spoel
Added
unit-t
e
st f
o
r
o
rientation restraints
o
utpu
t
.
commit
|
commitdiff
|
tree
2017-07-19
David van der S
p
oel
Remo
v
e
d
unneces
s
ary
static decl
a
r
ation
s
for comma
n
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van de
r
Spoel
Fixed test-order dependency in gmxpr
e
p
rocess
t
ests
.
commit
|
commitdiff
|
tree
2017-07-19
D
avid van der Spoel
Fix non-
r
eproduca
b
ility
o
f clusts
i
ze te
s
t
s
.
commit
|
commitdiff
|
tree
2017-05-01
Davi
d
v
a
n der Spoel
X
p
m test fo
r
gmx clu
s
t
s
ize
commit
|
commitdiff
|
tree
2017-03-12
D
a
vid van der Spoel
A
d
de
d
tests for gm
x
clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David van de
r
Spoel
R
emoves rogue prin
t
ing
to xvg file in
g
m
x
mindist
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
Fi
x
e
s
bug in
g
mx
s
o
l
vate wi
t
h -shel
l
that yi
e
ld
e
d
0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van
der S
p
oe
l
Fixes
S
EGV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
D
a
vid van der Spoel
Only print all
d
a
nglin
g
atoms with grompp
-v
commit
|
commitdiff
|
tree
2017-01-23
David van der S
p
oel
Added referen
c
e
for
d
ihedral function i
n
OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der Spoel
C
ou
p
le
o
f new quotes
commit
|
commitdiff
|
tree
2016-11-18
David v
a
n
der
Spoel
Added
f
i
rst
t
ests of bonded force funct
i
ons
.
commit
|
commitdiff
|
tree
2016-10-14
David va
n
d
er Spoe
l
F
ix
e
s some
m
e
m
o
r
y leak
s
a
s
soci
a
ted with testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der Spoel
Mod
u
lari
z
e electr
i
c
field handling
commit
|
commitdiff
|
tree
2016-09-27
David van der
S
poel
Fixed script
x
plor2gmx
.
pl to work
with GM
X
DATA
commit
|
commitdiff
|
tree
2016-09-26
Davi
d
van der Spoel
Fixes issue with Release
b
uild i
n
c
orrelation f
u
nctions
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
Mad
e
correlation fun
c
t
ion r
o
uti
n
e use std::vector
commit
|
commitdiff
|
tree
2016-09-05
D
a
vid van der Spoel
M
e
rge "Merge
b
ra
n
ch release
-
2016"
commit
|
commitdiff
|
tree
2016-08-24
D
a
vid
v
a
n de
r
Spoel
Added documentation
for she
l
l poten
t
ials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der Sp
o
el
Three new quot
e
s
.
commit
|
commitdiff
|
tree
2016-07-31
David van der Spoel
Merge "M
e
r
ge b
r
a
n
c
h release
-
5
-
1
into release-2
0
1
6
"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
Dav
i
d van
der Spoel
F
ixes incorrect cha
r
ges in OP
L
S/AA-L for HI
S
D and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van
der Spoel
Merge "Me
r
ge
branch rele
a
se-5-1 into releas
e
-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
avid van d
e
r S
p
oel
Introd
u
ce fatal
er
r
o
r
for
t
o
o few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van
der S
p
oel
M
ade gmx dos
w
ork ag
a
in
.
commit
|
commitdiff
|
tree
2016-06-22
Dav
i
d van der
Spo
e
l
Remov
e
d spurious
r_
i
j i
n
force for Mors
e
potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
a
vid van
der S
p
o
e
l
M
o
dify lmf
i
t
l
i
brary
t
o
av
o
i
d
clas
h
e
s
with o
t
h
e
r ve
r
s
ions
.
commit
|
commitdiff
|
tree
2016-03-23
David van
d
er
S
poel
Removed srenew that was making ar
r
ay smaller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Spoel
Fixed division by zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
Dav
i
d
van
d
er Spoel
Coup
l
e
of
new q
u
o
tes
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoel
Made norm
a
l mo
d
e
s
w
o
rk w
i
th she
l
ls and vsites
commit
|
commitdiff
|
tree
2015-11-24
D
a
vid van der Sp
o
el
Fixes n
e
wly intro
d
uced bug in make
_
ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van
d
er Sp
o
el
M
o
v
ed domdec struct
u
re
s
ou
t
of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van de
r
Spoel
Clean
u
ps i
n
legacyheader/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
an der Spoel
M
e
r
g
e
d
le
g
ac
y
h
ea
d
ers/
t
y
pes/qmmmre
c
.
h
int
o
m
dl
i
b/
q
m
m
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
i
d
v
an der Sp
o
el
Merged ge
n
born
.
h fro
m
l
e
g
acyheaders/ty
p
es into
m
dli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Moved legacyhe
a
der
s
/types/group
.
h to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
o
el
Merged legacyh
e
aders/types/ns
.
h and n
b
list
.
h
t
o
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der S
p
oe
l
Combine enums
.
h and names
*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged legacyheaders/nrnb
.
h and
t
y
p
es/nrnb
.
h to gmx
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
o
el
Mo
v
e
d
m
datom
.
h from lega
c
yheader/ty
p
es to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
v
i
d
v
a
n
der Spoel
Mo
v
ed l
e
gac
y
h
e
ad
e
rs/types/ener
g
y
.
h to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-15
David
v
an d
e
r Spoel
Merg
e
d
l
egacyheaders
/
t
ypes/inputrec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van
d
e
r Spoel
Merged legacyh
e
aders/types/st
a
te
.
h
in
t
o mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David
van der Spoel
R
epla
c
ed atom_id
b
y
int
.
commit
|
commitdiff
|
tree
2015-11-13
David van de
r
Spoel
Moved gen
b
o
r
n
.
h t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van der Sp
o
el
Moved t
x
t
d
u
m
p
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van d
e
r Spoe
l
Mov
e
d copyrite
.
* to fileio from gmx
l
i
b and
l
egacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
Da
v
id van der
S
poel
Move
d
inputrec
.
* from gmxlib and
l
egacyheade
r
s to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
David v
a
n der S
p
oel
Removed legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der
Spoel
Moved d
f
_history
u
tility
r
ou
t
ines from typedefs
to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der S
p
oel
R
e
placed
N
O
T
S
ET fro
m
typedef
s
.
h by local so
l
uti
o
ns
.
commit
|
commitdiff
|
tree
2015-10-23
Dav
i
d
van der Spoel
Remove
d
ene
r
gyhistory
c
o
d
e fro
m
typedefs
to
a
separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Mo
v
ed
pbc/cut-
o
ff re
l
ated u
t
ilities f
r
om typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Davi
d
v
an d
e
r Spoel
F
reed memory in l
e
gacy sta
t
istics ro
u
t
ines
.
commit
|
commitdiff
|
tree
2015-10-03
David van
d
er Spoe
l
R
emoved s
i
mpl
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van de
r
Spoe
l
R
e
mov
e
d simple
.
h
from nb_kernel_sse4_1_X
X
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id v
a
n der Spo
e
l
Removed simple
.
h from nb_
k
ernel_ss
e
2
_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van
d
er
S
poel
Removed simple
.
h
fr
o
m nb_kernel_c
a
nd
n
b_kernel_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der Spo
e
l
Removed
i
nclud
e
simple
.
h
f
rom nb_k
e
rnel
_
a
v
x_128_fma
_
XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der
S
p
oel
Removed simple
.
h from nb_kern
e
l_avx_256
_
XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
i
d v
a
n
d
er
S
poe
l
R
e
mo
v
e
d
output_env
_
t
,
n
ow using gmx_output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Davi
d
van
d
er Spoel
R
e
move
d
types
/
nrnb
.
h from typ
e
defs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van
d
e
r
Spoel
Remo
v
ed types/nblis
t
.
h a
n
d type
s
/nsgrid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van
d
er Spoel
Removed types/mdatom
.
h
from
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David
v
an
d
er Spoe
l
Removed types/inputrec
.
h f
r
o
m
typedefs
.
h
a
n
d r
e
l
eted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der
S
p
oel
Fi
x
es
b
ug i
n
the
c
omputat
i
o
n
of Coef
f
icient of
T
hermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David
v
an der Sp
o
el
Remove
d
types/f
o
r
c
ere
c
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David
v
a
n der Spoel
R
e
mov
e
d
include of
t
ypes/ifunc
.
h from typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid v
a
n
d
er Spoe
l
R
e
mov
e
d
f
our
i
ncludes f
r
om legacy
h
e
a
ders/typ
e
d
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van
der
S
poel
Removed
l
egac
y
header
s
/typ
e
s/commrec_
f
wd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
a
n
d
e
r Spoel
M
o
ved con
t
ent from mdrun
.
h
to sepa
r
ate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Removed <sys
/
types
.
h> and "types/con
s
tr
.
h" from ty
p
e
d
efs
commit
|
commitdiff
|
tree
2015-09-09
David va
n
de
r
Sp
o
e
l
Remove
d
fileio/trx
.
h from
t
ypedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van
d
er Spoel
M
ov
e
d
f
u
nctions operat
i
n
g
on forcerec to separate header
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
A
d
ded e
n
ergy (edr) file type to Options
headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
v
i
d van der Spoel
Added additional constr
u
cto
r
to S
t
ringStream
cl
a
ss
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van der Spoe
l
Made output fr
o
m du
m
p
i
n
g
n
eightb
o
rlists easier to rea
d
.
commit
|
commitdiff
|
tree
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