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Update instructions in containers.rst
2020-10-22
Christ
i
an
Bla
u
Change o
u
t
dated remdine references to gitlab
commit
|
commitdiff
|
tree
2020-10-21
Christi
a
n B
l
au
Ensure that gmx
c
ovar doe
s
n
o
t
access ind
i
c
es out
o
f
.
.
.
commit
|
commitdiff
|
tree
2020-10-21
C
hr
i
s
t
i
an
B
lau
Clarify that
m
dtut
o
r
i
als are no
t
prov
i
ded by
t
he grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2020-10-13
C
h
ristian Bla
u
Add
missing header in shake
t
o fix
m
a
c
clan
g
compilation
commit
|
commitdiff
|
tree
2020-10-09
Ch
r
istian Blau
Remove
dysfun
c
tio
n
al
QMMM inte
r
fa
c
e
p
t
5
commit
|
commitdiff
|
tree
2020-10-02
Chr
i
stian Blau
F
ix FEP lamb
d
a interpolat
i
on for reruns
commit
|
commitdiff
|
tree
2020-10-01
C
h
ri
s
tian B
l
au
Fi
x
the FEP
lambda
i
nt
e
rpolati
o
n
commit
|
commitdiff
|
tree
2020-09-22
Christian B
l
au
Nelder-Mead downhill simplex optimisation
commit
|
commitdiff
|
tree
2020-09-16
Christian
B
lau
Extend
u
ser docs on affi
n
e transform
a
tions for
densitie
s
commit
|
commitdiff
|
tree
2020-09-15
Chris
t
ian
B
l
au
All
c
oordinates in the densi
t
y
-guided-si
m
ulation group
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
Chr
i
stian Bla
u
Simpl
i
fy
a
nd fi
x
h
o
w
l
amb
d
a valu
e
s are
set
commit
|
commitdiff
|
tree
2020-09-08
Christian
B
lau
Al
l
ow densi
t
y-gui
d
ed simulations to tra
n
slate s
t
ructure
commit
|
commitdiff
|
tree
2020-09-07
Ch
r
is
t
i
a
n Blau
Fix cla
n
g
-f
o
rmat failure in coord
i
natetransformation
.
h
commit
|
commitdiff
|
tree
2020-09-07
C
h
ristian Blau
Implement affine co
o
rd
i
nate transformation
commit
|
commitdiff
|
tree
2020-09-04
Christian Blau
Strin
g
to array
c
on
v
ersion functions
commit
|
commitdiff
|
tree
2020-08-13
Ch
r
i
stian Blau
R
emov
e
superfl
u
ous ma
t
h utility
f
unctions
commit
|
commitdiff
|
tree
2020-08-10
Christia
n
Blau
Move density fitting checkpointing int
o
s
t
a
t
e
commit
|
commitdiff
|
tree
2020-08-07
Christian Blau
Fixed the
m
is-
f
ix
commit
|
commitdiff
|
tree
2020-07-07
Christian Blau
M
ove f
i
nal
i
sin
g
routine int
o
m
t
op
commit
|
commitdiff
|
tree
2020-07-02
C
h
r
i
s
t
ian Blau
Coordinate
t
ra
n
sforma
t
i
o
n on
s
ingle RVecs
commit
|
commitdiff
|
tree
2020-07-01
Christi
a
n Blau
Updated
t
he
change managemen
t
docum
e
n
t
ation
commit
|
commitdiff
|
tree
2020-04-17
Chr
i
stian
B
lau
pr
o
pos
e
d fix for redmine bug
#
3403
commit
|
commitdiff
|
tree
2020-03-16
Ch
r
istian Blau
Remove dy
s
funct
i
onal
Q
M
MM interfa
c
e
pt4
commit
|
commitdiff
|
tree
2020-03-16
Christian
B
lau
Rem
o
ve dysfunctional Q
M
MM interf
a
ce pt3
commit
|
commitdiff
|
tree
2020-03-16
Chris
t
i
an Blau
Remove d
y
sfunctiona
l
QMMM
interfa
c
e
pt2
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
R
e
move dysf
u
n
c
tional QMMM int
e
rfa
c
e
p
t1
commit
|
commitdiff
|
tree
2020-03-11
Christian Bla
u
Amend optional do
c
u
m
entation
commit
|
commitdiff
|
tree
2020-03-05
C
hristian Bla
u
Add fu
n
ctio
n
calls to MdModules to
s
i
gn up for notificat
i
ons
commit
|
commitdiff
|
tree
2020-03-05
Christian Blau
Split off implementation details of
MdMo
d
uleNotification
commit
|
commitdiff
|
tree
2020-03-04
Christian
Blau
Save e
x
cl
u
ded
non-bonded i
n
ter
a
c
t
io
n
s
in
.
tpr fi
l
e
commit
|
commitdiff
|
tree
2020-03-04
Chris
t
ian
B
lau
Add c
l
asshelp
e
r macro to forbi
d
copy, move and any
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
C
hristian Blau
Docu
m
ent density-fit cros
s
-correlat
i
on i
n
.
mdp options
commit
|
commitdiff
|
tree
2020-02-18
C
hristian Blau
Split
MdMo
d
ul
e
Notifications int
o
topics
commit
|
commitdiff
|
tree
2020-02-12
C
h
risti
a
n
Blau
Introduce re
a
dXvgData to
r
ead
x
vg d
a
ta into
std::vector
commit
|
commitdiff
|
tree
2020-01-31
C
h
r
i
stian Bl
a
u
Documentat
i
o
n
fix for
local
at
o
m s
e
t
data
commit
|
commitdiff
|
tree
2019-12-20
Christian Blau
Remove problemat
i
c output of gmx an
g
le
commit
|
commitdiff
|
tree
2019-12-15
Christ
i
an
B
l
au
F
ix densit
y
f
i
tting stalling
an
d
energies
commit
|
commitdiff
|
tree
2019-12-12
Christi
a
n Blau
D
ensityfitting - en
f
orce
s
imilarity incr
e
ase
with
a
daptive
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
C
hang
e
a
r
bitrary units to coun
t
s
in RMSD distan
c
e
d
istributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-05
Christia
n
Blau
R
elax cross-correlation tes
t
precision
commit
|
commitdiff
|
tree
2019-12-04
Christian Bl
a
u
R
emove cutoff-scheme gr
o
up f
r
om default
mdout
.
mdp output
commit
|
commitdiff
|
tree
2019-12-02
C
hri
s
ti
a
n Bl
a
u
Re
l
a
x
t
est tole
r
ance
f
or cross correlation
m
easure
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
C
h
r
i
sti
a
n Blau
Fix che
c
k-pointing for density g
u
ided simulat
i
on
s
commit
|
commitdiff
|
tree
2019-11-25
C
hristian Blau
F
i
x d
u
p
lica
t
e CONNECT records in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Chri
s
t
i
an Blau
Read
mr
c
density
map f
o
rmat with all end
i
a
nesses
.
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian B
l
au
Ch
e
c
k
mrc heade
r
for sanity
commit
|
commitdiff
|
tree
2019-11-24
Christian
B
lau
In
M
emorySerializer wi
t
h
end
i
aness
s
w
a
p
.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
S
toch
a
stic dyna
m
ics - docume
n
t th
a
t nsttcouple is ignored
commit
|
commitdiff
|
tree
2019-11-01
Christian Blau
Fi
x
cross-c
o
rrelati
o
n calcu
l
at
i
on in
s
tability
commit
|
commitdiff
|
tree
2019-10-22
Christ
i
an Bl
a
u
Fi
x
n
s
t in density-fitti
n
g modul
e
commit
|
commitdiff
|
tree
2019-10-18
C
h
rist
i
a
n Bl
a
u
Ma
n
u
a
l entry and
.
m
dp option for adaptive force scali
n
g
commit
|
commitdiff
|
tree
2019-10-18
C
hristian Bla
u
genion: prohibit io
n
pla
c
e
ment close to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refac
t
or
i
ng genion a
n
d adding test
commit
|
commitdiff
|
tree
2019-10-18
Christ
i
an Blau
A
d
a
pti
v
e
forc
e
sca
l
in
g
for de
n
sit
y
fitti
n
g
commit
|
commitdiff
|
tree
2019-10-16
Christian Blau
Expon
e
nti
a
l
moving average
commit
|
commitdiff
|
tree
2019-09-23
C
h
r
i
s
t
ian Bl
a
u
G
rompp error for mismatching
n
st fo
r
energy calul
a
tion
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christian Bl
a
u
Amend
m
ent
s
to density fitting manual secti
o
n
commit
|
commitdiff
|
tree
2019-09-22
Chr
i
stian Bl
a
u
A
dd
cross-corr
e
lat
i
on as
d
e
n
sity
simlarity measure
commit
|
commitdiff
|
tree
2019-09-19
C
h
ristian Blau
Chec
k
in
p
ut
record
a
l
so i
n
tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consist
e
ntly
c
hange dens
i
tyfitt
i
ng spr
e
ading w
e
ig
h
t
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Christian Blau
Add m
d
p option d
o
cume
n
tation for density f
i
tting
.
commit
|
commitdiff
|
tree
2019-09-12
C
h
risti
a
n
B
lau
Ma
n
ual entr
y
for d
e
n
s
ity guid
e
d si
m
ulations
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Add release note fo
r
density fit
t
ing
.
commit
|
commitdiff
|
tree
2019-09-11
Christia
n
Blau
Add com
m
ents to
g
rompp generated
.
mdp output for densityfitt
i
n
g
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
End to end test for
density
fitting
commit
|
commitdiff
|
tree
2019-09-11
C
h
risti
a
n
B
la
u
D
ensityfitti
n
g write int64_t
i
ndices in
s
tead of gmx
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Chris
t
i
an B
l
a
u
Use t
h
e current mass instead
of massA in density fitting
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Ch
r
i
s
tian Blau
Acco
u
n
t
for reference density origin sh
i
f
t
in pbc cor
r
ection
commit
|
commitdiff
|
tree
2019-09-09
Chr
i
stian
B
lau
Relativ
e
e
n
tropy as
density similarity mea
s
u
r
e
commit
|
commitdiff
|
tree
2019-09-09
Ch
r
istian Blau
A
dd option to normali
z
e
densities prior
t
o d
e
nsit
y
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
C
hristian Blau
A
dd
i
n
g every N-steps option
t
o
densityf
i
tting
commit
|
commitdiff
|
tree
2019-09-06
Ch
r
isti
a
n
B
l
a
u
Adding
e
ner
g
y output
f
ield for
density fitting
commit
|
commitdiff
|
tree
2019-09-06
C
h
ristian
B
lau
Periodi
c
b
oundary correction for density fitting
commit
|
commitdiff
|
tree
2019-09-05
C
h
r
i
s
t
i
an Bla
u
A
d
d reference den
s
i
t
y file option to dens
i
tyfitting
commit
|
commitdiff
|
tree
2019-09-04
C
h
ristian
Blau
Fix double
overloa
d
in LocalA
t
omSet
code when gmx:
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
R
e
ad
m
rc
f
i
l
e usin
g
file
n
a
m
e
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
Add
c
heckp
o
inti
n
g
for
MdModu
l
es
commit
|
commitdiff
|
tree
2019-08-30
Chr
i
sti
a
n
Bla
u
Cons
t
ructing local ato
m
sets
fo
r
d
e
nsity fit
t
ing
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian Blau
LocalAtomSet construction
wi
t
h vecto
r
s
of g
m
x::index
commit
|
commitdiff
|
tree
2019-08-30
Ch
r
istian Blau
Implem
e
nting the densit
y
fitting
f
orce provider
commit
|
commitdiff
|
tree
2019-08-27
Christian
Bla
u
Add density fitting
p
a
rame
t
ers
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Access to GaussTrans
f
orm3D
data
commit
|
commitdiff
|
tree
2019-08-27
Chris
t
ian
Blau
Add
i
ndex gr
o
up option to density fitting
commit
|
commitdiff
|
tree
2019-08-26
C
hrist
i
an Blau
Activ
a
tion
o
f
density
f
itting and move of module notific
a
tions
commit
|
commitdiff
|
tree
2019-08-25
C
h
ri
s
tian Blau
I
ndex groups for MdModules from grompp
commit
|
commitdiff
|
tree
2019-08-17
Chr
i
stian
Blau
Fi
x
segfa
u
lt with old tprs proc
e
ssing i
n
tern
a
l paramete
r
s
commit
|
commitdiff
|
tree
2019-08-15
Christian B
l
au
Move de
n
sityf
i
tting
option
s
and output into seperat
e
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
ristian
B
la
u
In
f
o class t
o
n
a
m
e and gene
r
ate the d
e
nsityfit
t
ing
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
C
h
ristian Blau
Inter
n
al pa
r
ameter s
t
o
rage for IM
D
Modules
commit
|
commitdiff
|
tree
2019-08-08
Chris
t
i
an Blau
Ha
r
m
o
n
i
z
e mrc density form
a
t extent
s
with
r
est
o
f cod
e
.
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
stian
B
la
u
Provi
d
e callbacks/no
t
ifications for MDModules
commit
|
commitdiff
|
tree
2019-07-26
C
h
ristian
B
lau
Fix failin
g
check-s
o
urce target on python3
.
6
commit
|
commitdiff
|
tree
2019-07-24
Chris
t
ian Blau
Fix HTML sou
r
ce docu
m
ena
t
ion error caused
b
y Gaus
s
T
ransform3D
commit
|
commitdiff
|
tree
2019-06-28
Chr
i
stian Bl
a
u
A
dd copy and m
o
v
e
o
perations
t
o den
s
ity similarity
commit
|
commitdiff
|
tree
2019-06-28
Chris
t
i
a
n
Blau
Add class to look up
de
n
sity fitting
amplitudes
commit
|
commitdiff
|
tree
2019-06-20
Christian Blau
Add coordinate scal
i
ng class
an
d
ext
e
nd Transla
t
eAnd
S
cale
commit
|
commitdiff
|
tree
2019-06-20
Chr
i
s
t
i
an
B
lau
All
o
w non-un
i
form Gaus
s
ians
commit
|
commitdiff
|
tree
2019-06-20
Christ
i
an Blau
Add BasicV
e
ctor sc
a
ling,
m
ax,
m
in and to
I
vec
commit
|
commitdiff
|
tree
2019-06-18
Christ
i
an
Blau
M
r
c
format header to latt
i
ce coordinate
tran
s
form
commit
|
commitdiff
|
tree
2019-06-18
Chr
i
stian Blau
Densi
t
y simi
l
arity meas
u
re
a
n
d gradie
n
t
commit
|
commitdiff
|
tree
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