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Further increase of tolerance for angles.
2019-02-08
David van der Spoel
Fu
r
th
e
r
increase of toleran
c
e for
a
ngles
.
commit
|
commitdiff
|
tree
2019-02-08
D
a
vid v
a
n der Sp
o
el
Increased toler
a
nce fo
r
angle
fu
n
c
t
i
ons
.
commit
|
commitdiff
|
tree
2019-02-08
David van
d
er Spoel
Increase to
l
erance in Angle
te
s
t
.
commit
|
commitdiff
|
tree
2019-02-08
David van d
e
r
Spoel
T
ests for listed fo
r
ce
p
o
t
en
t
ials
.
commit
|
commitdiff
|
tree
2019-01-26
David van d
e
r Sp
o
e
l
Fixe
d
s
o
m
e typos
i
n comments
.
commit
|
commitdiff
|
tree
2019-01-17
David van
der S
p
oe
l
A
l
low multip
l
e coordinate se
t
s in listed_forces test
.
commit
|
commitdiff
|
tree
2019-01-17
David van der Spo
e
l
Moved one reg
r
es
s
iont
e
st
to core gromacs
.
commit
|
commitdiff
|
tree
2019-01-14
David van der Spoel
MS
D
t
e
sts
for the
-
mol option
.
commit
|
commitdiff
|
tree
2019-01-11
D
a
v
i
d
van de
r
Spoel
Added low-level
t
es
t
s
f
or improper dihedrals
.
commit
|
commitdiff
|
tree
2018-12-31
David
v
an
d
er Spoel
Moved generi
c
sim
u
lationd
a
tabase code
t
o testutils
.
commit
|
commitdiff
|
tree
2018-12-30
Da
v
id van der S
p
oe
l
M
ov
e
d input files for
tests
t
o simula
t
ion datab
a
se
.
commit
|
commitdiff
|
tree
2018-12-30
Davi
d
van der Spoel
Implemented nati
v
e
nor
m
al mode
a
nalysis te
s
ts
.
commit
|
commitdiff
|
tree
2018-12-22
David van der Spoel
Revert "Remov
e
d t_topology from
g
mx msd"
commit
|
commitdiff
|
tree
2018-12-20
Dav
i
d van
der
Spoel
Re
m
oved t_to
p
ology
f
rom gmx msd
commit
|
commitdiff
|
tree
2018-12-05
David van der S
p
o
e
l
Ad
d
e
d
n
ew testing cod
e
for norm
a
l
mode analy
s
is
.
commit
|
commitdiff
|
tree
2018-12-04
D
avid van
d
e
r
S
p
oel
Small
u
pdate to md
r
un t
e
s
t
s
.
commit
|
commitdiff
|
tree
2018-12-04
David va
n
der
S
poel
Rem
o
ved gmx morph
commit
|
commitdiff
|
tree
2018-12-04
David
van der Spoe
l
Re
m
oved gmx dyndom
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r Spo
e
l
Removed gmx
a
nadock
commit
|
commitdiff
|
tree
2018-11-21
Dav
i
d van der
Spoel
M
e
r
g
e
b
r
a
n
c
h 'release-2019'
commit
|
commitdiff
|
tree
2018-11-18
David van der Spoel
Added citation for n
e
w
analysis
f
unctionality
.
commit
|
commitdiff
|
tree
2018-11-11
David v
a
n
d
er Spoel
Fix entropy calcul
a
tio
n
in gmx anaeig
commit
|
commitdiff
|
tree
2018-11-09
David
van d
e
r
Spoel
C
hange get_atom_index to allow mult
i
p
le m
o
l
ecules
.
commit
|
commitdiff
|
tree
2018-10-11
D
a
vid van
d
er Sp
o
el
Reinst
a
ted quasiharmonic entropy ca
l
culation
in
gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David van der Spoel
A
dded o
p
tion to gmx
n
m
eig
t
o p
r
int ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
David van
der Spoel
Let g
m
x nm
e
i
g print ther
m
ochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
D
av
i
d van der Spoel
Rename
d
entropy
.
* to thermo
c
hemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
a
vid van
de
r
Spoel
Split
o
ff entr
o
py calcul
a
tion to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
David van
d
er Spoel
Fi
x
es and updates
f
or xpl
o
r2g
m
l
.
pl and
ato
m
_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van de
r
Spoel
Fixe
d
check f
o
r
water
in
gen_
v
sit
e
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
Dav
i
d van
d
er Sp
o
el
New mdp i
n
put for electr
i
c fields
.
commit
|
commitdiff
|
tree
2017-10-30
Dav
i
d van d
e
r Spo
e
l
Fix
e
d mdp outpu
t
from
electric
field cod
e
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoe
l
Add
e
d option
-
water
tip
s
3
p
to
pd
b
2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van
der
S
poel
Split
o
f
f the N
M
R related analyse
s
f
rom gm
x
energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van
d
er Sp
o
el
F
ixe
d
missing entries in n
r
nb arra
y
s
.
commit
|
commitdiff
|
tree
2017-08-15
D
a
vid van der Spoel
Worked around missin
g
OpenMP implement
a
tion in
o
r
i
res
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Spoel
Fixed bug in gm
x
disres indexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
David van der Sp
o
e
l
Worked
a
ro
u
nd mis
s
in
g
OpenMP implemen
t
ation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
D
a
vid van der Spoel
Added unit-
t
est for orie
n
tatio
n
restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d
v
an der Spoel
R
emoved u
n
n
e
cessa
r
y static declar
a
tions for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoe
l
Fixed test-order dependen
c
y i
n
gmxp
r
eproc
e
ss tests
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
a
n
der Spoe
l
Fix
n
on-reproducab
i
lity of clust
s
ize tests
.
commit
|
commitdiff
|
tree
2017-05-01
David van der
Spoel
Xpm
t
est for gmx clustsize
commit
|
commitdiff
|
tree
2017-03-12
David van der Sp
o
el
Added
t
es
t
s for gmx clusts
i
ze
.
commit
|
commitdiff
|
tree
2017-03-04
Da
v
id v
a
n der Spo
e
l
Re
m
oves ro
g
ue printing to xvg
f
i
l
e
in g
m
x mindist
commit
|
commitdiff
|
tree
2017-02-27
D
a
v
i
d
van
d
er Spoel
Fixes bug
in gmx solvate with -shell
t
hat y
i
e
lded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
Da
v
id
van der Spoel
Fixes
SEGV
in gmx ord
e
r
.
commit
|
commitdiff
|
tree
2017-02-02
David van der Spoel
On
l
y prin
t
all dangling at
o
m
s
with grompp -v
commit
|
commitdiff
|
tree
2017-01-23
D
a
vid van der
S
poel
Added refe
r
e
n
c
e for dih
e
dral
f
unction in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der Spoe
l
Couple
o
f new quote
s
commit
|
commitdiff
|
tree
2016-11-18
David
v
an der Spoel
Added fir
s
t tests o
f
bond
e
d force functio
n
s
.
commit
|
commitdiff
|
tree
2016-10-14
D
a
vi
d
v
a
n der S
p
oel
Fixes
some memory leaks associated with test
i
ng ap
p
lied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
a
vid van der S
p
oel
Modularize
e
lectric field handling
commit
|
commitdiff
|
tree
2016-09-27
David van de
r
Spoel
F
i
xed
s
cript xplor2gmx
.
pl to
w
ork with
G
M
XDATA
commit
|
commitdiff
|
tree
2016-09-26
D
avi
d
v
a
n
de
r
Spoel
Fixes
i
ssue with Relea
s
e build in
c
orrelation fu
n
ction
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van d
e
r Spoel
Made corr
e
lation functi
o
n ro
u
tine use std::vector
commit
|
commitdiff
|
tree
2016-08-24
David
van der
Spo
e
l
Added documentatio
n
f
o
r she
l
l potentials
.
commit
|
commitdiff
|
tree
2016-08-03
David
van der Spoel
Three
n
e
w
quotes
.
commit
|
commitdiff
|
tree
2016-07-29
Davi
d
van der Spoel
Fix
e
s
incorrect cha
r
ge
s
i
n OPLS/A
A
-L for
HISD and H
I
S
E
commit
|
commitdiff
|
tree
2016-07-08
David van d
e
r Spoe
l
Intro
d
uce f
a
ta
l
error for too few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
D
a
vid va
n
der Spoel
Made
g
mx dos work again
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vid
v
a
n der Spoel
Removed spur
i
ou
s
r_ij in for
c
e
for Morse pote
n
ti
a
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Modi
f
y l
m
fit l
i
brary to avoid clash
e
s w
i
th o
t
her
versions
.
commit
|
commitdiff
|
tree
2016-03-23
David van
d
er Spoel
Removed sr
e
new that
w
as making
a
r
r
ay s
m
aller in
c
orrectly
.
commit
|
commitdiff
|
tree
2016-03-18
Da
v
id van de
r
Spoel
Fixe
d
d
i
v
ision by zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
Da
v
id v
a
n der
Sp
o
el
Cou
p
le of
ne
w
quotes
commit
|
commitdiff
|
tree
2016-01-07
David van der S
p
oe
l
Made normal modes work with shells and
v
site
s
commit
|
commitdiff
|
tree
2015-11-24
David
v
an de
r
S
p
oel
Fix
e
s newly introdu
c
e
d bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
Davi
d
van der
S
poel
Mo
v
ed domdec str
u
ctures out of comm
r
ec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der
S
p
o
el
Cleanups in legacyh
e
ad
e
r/typ
e
s/comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
S
poel
Merged
l
egacyhead
e
rs/types/qmmm
r
ec
.
h into mdli
b
/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van d
e
r Spoel
Merged ge
n
bo
r
n
.
h from lega
c
yheaders/type
s
into mdli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der Spoel
Moved legacyhe
a
ders/type
s
/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der
S
po
e
l
Mer
g
ed legacyheaders
/
types/
n
s
.
h and nbl
i
st
.
h
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Spoel
Combine enu
m
s
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er
Spoel
Merged
l
egacyheade
r
s/nrnb
.
h a
n
d types/nrnb
.
h to gm
x
lib
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
e
r Spoel
M
oved m
d
atom
.
h from legacyheader/types
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid v
a
n
d
er Spoel
Moved legacyheaders/typ
e
s/energy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoe
l
Mer
g
ed l
e
gacyheaders/
t
ypes/i
n
putr
e
c
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
avid van der Spoel
Merged le
g
acy
h
eaders/
t
yp
e
s/state
.
h into
m
d
t
ypes/
s
tate
.
h
commit
|
commitdiff
|
tree
2015-11-13
Da
v
id van der Spoel
Replaced a
t
om
_
id by in
t
.
commit
|
commitdiff
|
tree
2015-11-13
David
v
a
n der Spoel
M
o
ve
d
genbor
n
.
h
to m
d
lib
commit
|
commitdiff
|
tree
2015-11-12
David
v
a
n der
Spoel
M
oved txtd
u
mp
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David
v
a
n d
e
r Spoel
M
o
ved c
o
pyrite
.
* to f
i
leio from
gmxlib
a
n
d legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der Sp
o
e
l
M
o
ved in
p
u
t
rec
.
* from gmxlib and
legacyheaders to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-10
David va
n
der Sp
o
el
Removed legacyhe
a
ders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
D
avi
d
van de
r
Spo
e
l
Move
d
df_
h
istory utility r
o
u
tines from typ
e
d
efs
to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
avid van der S
p
oel
Replaced
N
OTSET from
t
yped
e
fs
.
h
by loca
l
solutions
.
commit
|
commitdiff
|
tree
2015-10-23
Da
v
id van der Spo
e
l
Remove
d
e
nergyhist
o
ry code
from typedefs to a
s
eparate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
Davi
d
van de
r
Spoel
Mov
e
d pbc/cut-off related utili
t
ies from typedefs t
o
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
avid van der Sp
o
el
F
reed m
e
m
or
y
in
legacy statistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David van der Spoel
Remov
e
d simp
l
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David va
n
der S
p
oel
Remo
v
ed s
i
mple
.
h fro
m
nb_k
e
rnel_
s
se4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David
v
an
de
r
S
p
oel
Removed sim
p
le
.
h from nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
emove
d
simple
.
h from
nb_kernel_c and nb_kernel_spar
c
64_
h
pc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Dav
i
d
v
a
n der Spoel
R
e
moved incl
u
de simple
.
h from
nb_kernel
_
av
x
_128_fm
a
_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoel
Remov
e
d s
i
m
p
le
.
h from n
b
_
kerne
l
_a
v
x_256_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avi
d
v
a
n der
S
p
oel
Removed output_env_t, now using gm
x
_
o
u
tput_env_
t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spoel
Removed types/
n
rnb
.
h
from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
avid
v
an der Spoel
Remove
d
types/nb
l
ist
.
h and typ
e
s
/
n
s
grid
.
h fro
m
type
d
efs
.
h
commit
|
commitdiff
|
tree
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