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Added new testing code for normal mode analysis.
2018-12-05
David van der
S
poe
l
Added new
test
i
ng code f
o
r normal mo
d
e analysis
.
commit
|
commitdiff
|
tree
2018-12-04
David van der S
p
oel
Small update to m
d
run tests
.
commit
|
commitdiff
|
tree
2018-12-04
D
avid van der S
p
oel
Removed gmx morph
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
van der S
p
oel
Remove
d
gmx dynd
o
m
commit
|
commitdiff
|
tree
2018-12-04
David
v
an der Spoel
Rem
o
v
ed gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
Da
v
i
d
van der
S
poel
Merge branch 'relea
s
e-201
9
'
commit
|
commitdiff
|
tree
2018-11-19
Mark A
b
raham
Fix
inef
f
icient she
l
l minimization
commit
|
commitdiff
|
tree
2018-11-18
David van der Spoel
Added citation f
o
r ne
w
analysis functionality
.
commit
|
commitdiff
|
tree
2018-11-08
Paul
Bauer
Actuall
y
fix gmx
helix segm
e
nta
t
i
on fau
l
t
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
Impr
o
ve ro
b
ustn
e
ss of en
d
-to-end testin
g
commit
|
commitdiff
|
tree
2018-06-22
Mark Abra
h
a
m
Up
d
ate energy and tr
a
jectory f
r
ame types
commit
|
commitdiff
|
tree
2018-06-12
Mar
k
Abraham
Prepare
for GROMACS 201
9
release notes
commit
|
commitdiff
|
tree
2018-06-12
D
a
v
id van der Spoel
Le
t
gmx nmeig print therm
o
chemistry
.
commit
|
commitdiff
|
tree
2018-03-16
David
van
der
S
poe
l
Split off entropy calculation to separate
file
.
commit
|
commitdiff
|
tree
2018-01-04
Erik
L
indahl
Improve
f
rame time/step handling in
trjc
o
nv
commit
|
commitdiff
|
tree
2018-01-03
Erik
Li
n
dahl
Fix trjcon
v
f
o
r tdump<frame tim
e
step
commit
|
commitdiff
|
tree
2018-01-01
Erik Lin
d
ahl
Fix gmx den
s
ity for non-mass calculations
commit
|
commitdiff
|
tree
2017-12-28
David van der Spoel
Fixes
and upda
t
es for xplor2gml
.
pl and
a
tom_nom
.
tbl
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Fixed
mdp output
from electric fi
e
ld code
.
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iupinov
Re
m
ove unused PM
E
grid dump debug
f
u
nctions
commit
|
commitdiff
|
tree
2017-10-17
David va
n
der Spoel
Fixed missing entries in nrnb
a
rrays
.
commit
|
commitdiff
|
tree
2017-09-04
Teemu Murt
o
la
Introduce self
-
pai
r
s
s
earch in n
b
search
commit
|
commitdiff
|
tree
2017-09-04
Tee
m
u Murtola
R
efac
t
or analysis nbse
a
rch tes
t
s
commit
|
commitdiff
|
tree
2017-08-09
Roland
Schulz
Use tabl
e
Ewa
l
d
f
o
r
S
k
ylake
commit
|
commitdiff
|
tree
2017-08-03
David van der
S
poe
l
F
ixed bug in gmx d
i
sres indexing a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-02
B
e
r
k
Hess
Ma
k
e loop variables
i
n orires
.
cpp local
commit
|
commitdiff
|
tree
2017-08-02
Be
r
k
He
s
s
A
dd
check fo
r
nr of or
i
entation restraints
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d van der Spoel
Fi
x
ed test-or
d
er dependency in gmx
p
reproc
e
ss t
e
sts
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
an der Spoel
Fix non-reproducability
o
f clustsize
tests
.
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kutzner
Min
o
r h
e
ad
e
r file
c
leanup i
n
ED, IMD and Comp
E
L
mod
u
les
commit
|
commitdiff
|
tree
2017-04-22
M
a
rk
A
brah
a
m
Clean up memo
r
y
usage with oenv and xvg writing
commit
|
commitdiff
|
tree
2017-03-13
Te
e
mu Mur
t
o
l
a
I
mprove optio
n
support &
t
ests
f
o
r key-value trees
commit
|
commitdiff
|
tree
2017-03-13
Teemu M
u
r
t
o
l
a
Remov
e
m
a
n
ual alignment from
I
nMemorySer
i
ali
z
er
commit
|
commitdiff
|
tree
2017-03-12
Teemu Murtol
a
C
o
n
s
istent TextW
r
iter
t
r
ai
l
ing whit
e
sp
a
ce
h
a
n
dling
commit
|
commitdiff
|
tree
2017-03-12
David
van der Spoel
A
dded test
s
fo
r
gmx clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
Vedran Milet
i
ć
Doc
u
ment
t
ha
t
we now support AMD GCN on
M
esa/LLVM
commit
|
commitdiff
|
tree
2017-02-28
B
erk Hess
Add load balance fractio
n
to
DLB print
commit
|
commitdiff
|
tree
2017-02-28
T
eemu Murtola
More
d
ocumen
t
ati
o
n
f
or key-val
u
e tre
e
s
commit
|
commitdiff
|
tree
2017-02-27
David
v
a
n
der Spoel
F
i
xes bug in gmx s
o
lvate
with
-shell
that
yie
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-09
Aleksei Iu
p
inov
Add i
n
i
t
i
alizatio
n
to dvdlambda
i
n
b
onded f
o
rces te
s
t
s
commit
|
commitdiff
|
tree
2017-02-08
M
ark Ab
r
aham
R
e
move docs for un
i
mplemented t
r
j
c
o
n
v -clu
s
te
r
center
commit
|
commitdiff
|
tree
2017-02-02
Mark Ab
r
aham
C
larify use
o
f
t
au-p and pcoupltype
commit
|
commitdiff
|
tree
2017-01-30
M
ark
A
braham
Don
'
t
p
rint inva
l
i
d p
e
r
f
orm
a
nce data
commit
|
commitdiff
|
tree
2016-12-14
Mark Abr
a
h
am
Fix mislead
i
n
g
parallelizat
i
on docs for gmx wh
a
m
commit
|
commitdiff
|
tree
2016-11-21
Aleksei Iupinov
Move hardco
d
ed PME g
r
id indexin
g
con
s
tants into header
commit
|
commitdiff
|
tree
2016-11-18
D
a
vid va
n
der Sp
o
el
A
dded first tests of
bonde
d
f
orce functions
.
commit
|
commitdiff
|
tree
2016-11-16
Mark Abraham
Enha
n
ced Arr
a
y
R
e
f
commit
|
commitdiff
|
tree
2016-11-16
Mark Abraham
Created paddedvec
t
or
.
h
commit
|
commitdiff
|
tree
2016-10-24
T
e
emu Murt
o
la
Electric fiel
d
mdp pa
r
sing us
i
ng
o
ptions
commit
|
commitdiff
|
tree
2016-10-24
Teemu
M
urtol
a
Support for default values from
Op
t
ions to Key
V
alueTree
commit
|
commitdiff
|
tree
2016-10-14
Berk Hess
Apply Berendsen P-co
u
ple at nstpcouple steps
commit
|
commitdiff
|
tree
2016-10-14
Teemu
Murtola
U
se gmx_mtop_t i
n
s
e
lections, part 3
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Getter for mapp
e
d
p
a
ths from KeyValueTre
e
Transform
commit
|
commitdiff
|
tree
2016-10-08
Berk Hess
Add
read
C
o
n
fAndTopology
commit
|
commitdiff
|
tree
2016-10-03
Philip Loche
E
W
3DC for non-n
e
utra
l
sy
s
tems
commit
|
commitdiff
|
tree
2016-10-01
Berk Hess
Fix
i
nputrec init
i
a
l
ization in 4 t
o
ols
commit
|
commitdiff
|
tree
2016-09-29
Be
r
k
H
ess
Use std::vector in t_s
t
ate
commit
|
commitdiff
|
tree
2016-09-29
Be
r
k Hess
Add
f
l
ags for opt
i
onal t_atoms
e
nt
r
ies
commit
|
commitdiff
|
tree
2016-09-20
Berk Hes
s
Re
m
ove s
t
a
te d
u
plicat
i
on in
seria
l
run
s
commit
|
commitdiff
|
tree
2016-09-20
David van der
Spoe
l
Made correl
a
tio
n
f
u
n
c
t
io
n
routine use
std:
:
v
ector
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Made distance
r
estr
a
i
n
t
s
work
wi
t
h
t
hreads and
D
D
commit
|
commitdiff
|
tree
2016-09-15
Aleksei Iu
p
inov
Move the PME Ewald coefficien
t
s to t
h
e PME s
t
r
u
cture
commit
|
commitdiff
|
tree
2016-09-13
Roland Schul
z
Tidy: m
o
dernize-use-e
m
place
commit
|
commitdiff
|
tree
2016-09-13
Berk Hes
s
Change ED and swapst
a
t
e
to pointers in t_state
commit
|
commitdiff
|
tree
2016-09-11
Vedran Miletić
Print O
p
enCL error strin
g
instead of error cod
e
commit
|
commitdiff
|
tree
2016-09-10
Berk H
e
ss
Remove conti
n
uation from conve
r
t_t
p
r
commit
|
commitdiff
|
tree
2016-09-10
Aleksei Iupi
n
ov
F
ix PME data destr
u
ctor
not being called
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Merge "Merge
b
ran
c
h
release-
2
0
1
6"
commit
|
commitdiff
|
tree
2016-08-27
Szilárd Páll
Make ASAN/TSAN/MSAN
bui
l
d types easier to discover
commit
|
commitdiff
|
tree
2016-08-27
Ma
r
k Abraham
St
o
p us
i
ng gmx_f
a
tal in
g
romp
p
commit
|
commitdiff
|
tree
2016-08-27
Te
e
mu Murtola
Support
K
e
y
ValueTree
o
bje
c
ts i
n
refdata
commit
|
commitdiff
|
tree
2016-08-27
Berk Hess
Reduce rounding errors in
SETTLE
commit
|
commitdiff
|
tree
2016-08-27
R
o
land Sc
h
ulz
Fix bu
i
ld with GMX_USE_TNG=off
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
A
d
de
d
d
oc
u
mentatio
n
for she
l
l potentia
l
s
.
commit
|
commitdiff
|
tree
2016-07-31
Dav
i
d van der Spoel
Mer
g
e
"
Merge
b
ranch release-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Ved
r
an Miletić
Print working dir bef
o
re co
m
man
d
line
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
M
e
rge "Merge
b
r
anch
r
ele
a
se-
5
-1
into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Szilá
r
d Páll
User guide
clarif
i
cations
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Relax pull
P
BC chec
k
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add gr
o
mpp chec
k
f
o
r pull gro
u
p
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made gmx
dos
work agai
n
.
commit
|
commitdiff
|
tree
2016-06-26
Ber
k
Hess
Fix vsite bug with
M
PI+OpenM
P
commit
|
commitdiff
|
tree
2016-06-21
B
e
rk Hess
F
ix
bu
g
w
ith
f
bposres+MPI+OpenMP
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
A
dd gromp
p
check for u
n
b
ound
a
toms
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fix constants, units and conversio
n
factors
commit
|
commitdiff
|
tree
2016-03-23
Da
v
id van der Spoel
R
e
moved srenew tha
t
w
as mak
i
n
g
arr
a
y s
m
aller i
n
co
r
r
e
c
tly
.
commit
|
commitdiff
|
tree
2016-01-20
David
v
an
d
er Spoel
Coupl
e
o
f
new quotes
commit
|
commitdiff
|
tree
2015-12-09
T
e
emu Murt
o
la
Split txtdump
.
*, part 1
commit
|
commitdiff
|
tree
2015-12-05
Magnus Lundborg
Write forces and vel
o
cities
t
o
com
p
re
s
sed TNG
.
commit
|
commitdiff
|
tree
2015-11-24
D
a
vid
v
an der Spoel
Fixes newly introduc
e
d bug in
m
ake_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Spoel
M
oved domdec
s
tructure
s
out
o
f c
o
mmrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoel
Cleanup
s
in legac
y
header/types
/
commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van
der Spoel
M
e
rged legacyheaders/ty
p
es/qmmmrec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spo
e
l
Move
d
legacyheaders/t
y
p
es/group
.
h
t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
S
p
oel
M
e
rge
d
legacyheader
s
/types/ns
.
h an
d
nbl
i
s
t
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Comb
i
ne enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
Mark
A
braham
S
p
l
i
t
wallcy
c
le
i
n
t
erfa
c
e
commit
|
commitdiff
|
tree
2015-11-20
David van
der Sp
o
el
Merged legacy
h
eaders/nrnb
.
h and type
s
/nrnb
.
h to gm
x
lib
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der S
p
oe
l
Mov
e
d
m
datom
.
h from l
e
g
a
cyheade
r
/typ
e
s to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-15
David
van der Spoel
M
er
g
ed legacyheade
r
s/typ
e
s/
s
tate
.
h i
n
to
mdtypes/state
.
h
commit
|
commitdiff
|
tree
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