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Add tests for gmx mindist
2019-01-17
David van d
e
r Spoel
Allow mu
l
tiple coordinate sets
i
n
l
i
sted_forc
e
s test
.
commit
|
commitdiff
|
tree
2019-01-17
Davi
d
va
n
der Spo
e
l
Moved one regressiontest to core gromacs
.
commit
|
commitdiff
|
tree
2019-01-14
D
avid van der Spoel
MSD t
e
sts for th
e
-mol op
t
ion
.
commit
|
commitdiff
|
tree
2019-01-11
David va
n
der S
p
oel
Added low-l
e
vel tests for improper dihedra
l
s
.
commit
|
commitdiff
|
tree
2018-12-31
D
a
vid van
d
er
Spoe
l
Moved
g
ener
i
c simu
l
ationdata
b
ase code
to
t
e
s
tutils
.
commit
|
commitdiff
|
tree
2018-12-30
David van der S
p
oe
l
Moved in
p
ut
fil
e
s for test
s
to si
m
ul
a
tio
n
d
a
tabas
e
.
commit
|
commitdiff
|
tree
2018-12-30
David v
a
n der S
p
oel
Implemented nati
v
e
normal mode analysis tes
t
s
.
commit
|
commitdiff
|
tree
2018-12-22
Dav
i
d van d
e
r Spoel
Revert
"R
e
moved
t
_topology from gmx msd"
commit
|
commitdiff
|
tree
2018-12-20
David van der Spoel
Remov
e
d t
_
topology from
g
m
x m
s
d
commit
|
commitdiff
|
tree
2018-12-05
Da
v
id van der S
p
oel
A
dde
d
new test
i
ng code for normal
m
ode
a
nalysis
.
commit
|
commitdiff
|
tree
2018-12-04
D
avid
v
a
n der Spoel
Sm
a
l
l
u
p
date to mdrun test
s
.
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
van der Spoel
Removed
g
m
x morph
commit
|
commitdiff
|
tree
2018-12-04
David
v
an der
S
poel
Removed gmx dyndom
commit
|
commitdiff
|
tree
2018-12-04
Da
v
id van de
r
Spoel
Rem
o
ved gmx anado
c
k
commit
|
commitdiff
|
tree
2018-11-21
David van der Spoel
Me
r
g
e branch 'releas
e
-2019'
commit
|
commitdiff
|
tree
2018-11-18
David
v
an
der S
p
oel
Added
c
it
a
ti
o
n
for
n
ew analysis f
u
ncti
o
nality
.
commit
|
commitdiff
|
tree
2018-11-11
David van
d
er Sp
o
el
Fix en
t
ropy calculat
i
on in gmx anaeig
commit
|
commitdiff
|
tree
2018-11-09
Da
v
id van der
S
poel
Change get_
a
tom_index to allow multiple molecules
.
commit
|
commitdiff
|
tree
2018-10-11
David van der
Spoel
Reinstated quasih
a
rmonic entropy calculation in
g
mx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David v
a
n der Spoel
Added option to
gmx nmeig
to pri
n
t
Z
P
E
.
commit
|
commitdiff
|
tree
2018-06-12
David van der Spoel
Let
g
m
x
nmeig print t
h
ermochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
Da
v
id van der Spoel
Ren
a
med entropy
.
*
to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
av
i
d van
d
er Spoel
Split o
f
f ent
r
opy c
a
lcul
a
tio
n
to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
D
a
vid van der Sp
o
el
Fixes and upda
t
es for
x
plor2gml
.
p
l a
n
d atom
_
nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van
d
e
r
S
p
oel
Fixed check for
wa
t
er in gen_
v
s
ite
.
c
pp
commit
|
commitdiff
|
tree
2017-11-02
David van der Spoel
N
e
w md
p
input for electric f
i
elds
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
an der S
p
oel
F
ix
e
d m
d
p
ou
t
pu
t
from
e
lectric field code
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
A
d
ded option -wa
t
er tips3p to pdb
2
gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van
d
er Sp
o
e
l
S
p
lit off th
e
N
M
R related analyses f
r
om g
m
x energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
avid van der Spo
e
l
Fixed missing ent
r
ies
in nrnb a
r
r
a
ys
.
commit
|
commitdiff
|
tree
2017-08-15
Da
v
id van der Spoel
Work
e
d around missi
n
g OpenMP impl
e
mentatio
n
in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David va
n
der
Spoel
Fixed bug in gmx d
i
s
re
s
i
nd
e
xin
g
a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-02
D
a
vid
va
n
der
S
p
o
e
l
Worked around miss
i
ng Ope
n
MP implementati
o
n
in orire
s
.
commit
|
commitdiff
|
tree
2017-07-28
Da
v
i
d
van d
e
r Sp
o
el
Added unit-test
f
o
r
orientation restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
David va
n
d
e
r Spo
e
l
Rem
o
ved
u
nnecessary static declarations for c
o
m
mand
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van
d
er Spoel
Fixed te
s
t
-
order dependency in gmxp
r
eprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoe
l
Fix non-reproduc
a
bility of clustsize test
s
.
commit
|
commitdiff
|
tree
2017-05-01
David van der Spoe
l
Xpm te
s
t f
o
r gmx clu
s
t
s
ize
commit
|
commitdiff
|
tree
2017-03-12
Dav
i
d
v
an de
r
Sp
o
el
Added tests for gmx clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoe
l
Remov
e
s rogue printing to
xvg file i
n
g
mx mindist
commit
|
commitdiff
|
tree
2017-02-27
David van d
e
r Spoel
Fixes bug in gmx
s
olvate with -shell
t
h
at yie
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van
der
S
poel
Fixes S
E
GV in
g
mx order
.
commit
|
commitdiff
|
tree
2017-02-02
David van
de
r
Spoe
l
O
n
ly print a
l
l dangl
i
ng
a
toms with g
r
o
mpp -v
commit
|
commitdiff
|
tree
2017-01-23
David va
n
de
r
Spoel
Added
r
eference for
d
i
h
edral fu
n
ction in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
D
avi
d
va
n
der S
p
oel
C
o
uple of new q
u
o
t
es
commit
|
commitdiff
|
tree
2016-11-18
Davi
d
van d
e
r Sp
o
el
A
dded first tests
o
f b
o
nded force functions
.
commit
|
commitdiff
|
tree
2016-10-14
D
a
vid van
d
er Spo
e
l
Fixes some m
e
mory
l
eaks associated with tes
t
ing app
l
ied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
Dav
i
d v
a
n
der Spoel
Mo
d
ularize electri
c
field handling
commit
|
commitdiff
|
tree
2016-09-27
David van der Spoe
l
Fixed sc
r
i
pt
x
plor2gm
x
.
pl to wo
r
k with
G
MXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van der Sp
o
el
F
ixes is
s
ue with Rel
e
a
s
e
buil
d
in correlation function
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van de
r
Spoel
Made corr
e
lation functio
n
rou
t
ine
use std::vec
t
or
commit
|
commitdiff
|
tree
2016-09-05
Dav
i
d van d
e
r Spoel
Merge
"
M
e
r
ge
b
ranch rel
e
ase-
2
016
"
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
Ad
d
ed
do
c
umentation for
s
he
l
l potent
i
als
.
commit
|
commitdiff
|
tree
2016-08-03
Da
v
id
v
an der
S
p
oel
Three new
quote
s
.
commit
|
commitdiff
|
tree
2016-07-31
David
v
a
n
d
er Spoel
Me
r
ge "Me
r
g
e
br
a
nch relea
s
e-5-1 i
n
to
r
e
lease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
Da
v
i
d van der Spoel
Fixes incorrect
charges in OPLS/AA-L
f
or
HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David v
a
n de
r
Spoe
l
Mer
g
e
"Mer
g
e branch release-5-1
i
nto release
-
20
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
avid van de
r
Spoel
Introduce fata
l
er
r
or for too few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van
d
er Spoel
Made g
m
x dos wo
r
k a
g
ain
.
commit
|
commitdiff
|
tree
2016-06-22
David van der Spoel
R
e
mo
v
e
d
spurious r_ij in forc
e
fo
r
Morse pot
e
nt
i
al
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van de
r
Spo
e
l
Modify lmf
i
t library to
avoid clashes with ot
h
er v
e
rsions
.
commit
|
commitdiff
|
tree
2016-03-23
D
avi
d
v
an der
S
p
oel
Remov
e
d srenew that was making array smaller incorre
c
t
l
y
.
commit
|
commitdiff
|
tree
2016-03-18
Dav
i
d
va
n
der
Spoel
Fixed division by
z
ero i
n
polari
z
e
.
commit
|
commitdiff
|
tree
2016-01-20
Da
v
id van der Spoel
Couple of
new quote
s
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoe
l
Mad
e
normal modes work with
shells and
v
si
t
es
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fix
e
s newly introduced bug in
m
ake_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David
v
an der Sp
o
el
Moved
d
omd
e
c structures o
u
t of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoel
Cl
e
anup
s
in le
g
acyheader/
t
ypes/commr
e
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
an der Spoel
Merged
legac
y
headers/types/qmmmr
e
c
.
h into mdlib
/
qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
Davi
d
v
a
n der Spoel
M
e
rged genborn
.
h
f
ro
m
l
e
gacyhe
a
d
ers/types into mdli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der Spoel
Moved le
g
a
c
yh
e
aders/
t
y
p
es/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoe
l
M
erged legacyheaders/types/ns
.
h and nbl
i
st
.
h
to md
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der Spoel
Combine
enums
.
h and nam
e
s*
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der Spoel
Merged legacyheaders/nrnb
.
h and types/nrnb
.
h to
g
m
x
l
i
b
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved mdatom
.
h
from l
e
ga
c
yheader/typ
e
s to
m
d
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
p
o
el
M
oved legacyheaders/types/ene
r
gy
.
h to
md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van der
S
po
e
l
Merge
d
le
g
acyhea
d
ers/types/
i
np
u
trec
.
h into mdtype
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der S
p
oe
l
Merged legacy
h
e
a
de
r
s/types/state
.
h int
o
mdtypes/s
t
ate
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der
S
poel
Replaced atom
_
id
b
y int
.
commit
|
commitdiff
|
tree
2015-11-13
David
v
an der Sp
o
el
Move
d
ge
n
born
.
h to mdl
i
b
commit
|
commitdiff
|
tree
2015-11-12
Dav
i
d
va
n
der Spoel
Moved txtdump
.
* to
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David va
n
der
S
poel
Moved copyrite
.
* to
fileio fr
o
m gmxlib and
l
egacyhea
d
er
s
.
commit
|
commitdiff
|
tree
2015-11-11
David van der S
p
oel
Mov
e
d i
n
putrec
.
* from gmxlib and
l
egacyh
e
aders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van d
e
r Spoel
Removed legacyheader
s
/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Davi
d
van der Spoel
Move
d
df_history utility routines
f
rom typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Dav
i
d van der Spoe
l
Replaced NOTSET from typedefs
.
h by local solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David van d
e
r Spoel
Remov
e
d
energyhistory code from typedefs to
a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spo
e
l
Moved pbc/cut-o
f
f relate
d
util
i
ties
f
r
o
m typed
e
fs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Sp
o
e
l
Freed memory in legacy s
t
atis
t
i
cs ro
u
tines
.
commit
|
commitdiff
|
tree
2015-10-03
David van der Spoel
Removed simpl
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
v
a
n
der Spoe
l
Re
m
oved simple
.
h
from
nb
_
k
ernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
va
n
der
Sp
o
el
Re
m
ove
d
simple
.
h from
n
b
_ker
n
e
l
_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoel
Remove
d
s
imple
.
h
from n
b
_kernel_c and
nb_kernel_sparc6
4
_
h
pc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id v
a
n der S
p
oel
Re
m
oved include simple
.
h from nb_kernel_avx_128_fma_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David va
n
der Spoel
Removed simple
.
h fr
o
m nb_ker
n
el_avx_
2
56_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van d
e
r Spoel
R
emoved
output_env_t,
n
ow using gmx_o
u
tput_en
v
_t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van
d
er Spoel
R
e
moved types/
n
r
n
b
.
h from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van
d
e
r
Spoel
Re
m
oved type
s
/nb
l
ist
.
h a
n
d t
y
pes/ns
g
rid
.
h from
t
ype
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Da
v
i
d van
der Sp
o
e
l
Remo
v
e
d
t
y
pes/mdato
m
.
h from typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Da
v
id v
a
n der Spoe
l
Removed types/inputrec
.
h from typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
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