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Fix small leaks in do_md cleanup
2018-12-26
K
ev
i
n Boyd
Fix s
m
all
l
eaks in do_md cleanup
commit
|
commitdiff
|
tree
2018-12-22
David van d
e
r
Spoel
Revert "Removed t_topol
o
gy from gmx msd"
commit
|
commitdiff
|
tree
2018-12-05
David
v
a
n
d
e
r Sp
o
el
Ad
d
ed new
t
esting code
f
o
r no
r
mal
mod
e
an
a
ly
s
i
s
.
commit
|
commitdiff
|
tree
2018-12-04
David van der
S
p
o
el
Small upd
a
te to
mdrun tests
.
commit
|
commitdiff
|
tree
2018-12-04
David va
n
der Spoel
Removed gmx
m
o
rph
commit
|
commitdiff
|
tree
2018-12-04
Dav
i
d van de
r
Spoel
R
e
mov
e
d gmx dyndo
m
commit
|
commitdiff
|
tree
2018-12-04
David van der
S
p
o
e
l
Removed gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
David van der
S
p
o
el
M
erg
e
branch 'release-2019'
commit
|
commitdiff
|
tree
2018-11-19
Mar
k
Abraham
Fix ineffici
e
nt shel
l
minimization
commit
|
commitdiff
|
tree
2018-11-18
Dav
i
d
van der Spoel
Added citatio
n
for new anal
y
sis functi
o
nality
.
commit
|
commitdiff
|
tree
2018-11-08
Paul Bau
e
r
A
ctua
l
ly
fix gmx he
l
ix
seg
m
entation fault
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
I
mprove ro
b
ustness of e
n
d-t
o
-end testing
commit
|
commitdiff
|
tree
2018-06-22
M
a
rk Abraham
Up
d
ate energy
and
t
r
ajectory fr
a
me t
y
p
e
s
commit
|
commitdiff
|
tree
2018-06-12
M
ark A
b
r
a
ham
Prepar
e
fo
r
GROMACS 2019 re
l
ease notes
commit
|
commitdiff
|
tree
2018-06-12
D
a
vid van
d
e
r
Spoel
Let gmx
nmeig print the
r
mochemistry
.
commit
|
commitdiff
|
tree
2018-03-16
David van der Spoel
Spli
t
off
entropy calculati
o
n
t
o separate file
.
commit
|
commitdiff
|
tree
2018-01-04
E
rik Lindahl
Improve fram
e
time
/
step handlin
g
i
n
trjconv
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindah
l
Fix trjc
o
nv fo
r
td
u
mp<frame timeste
p
commit
|
commitdiff
|
tree
2018-01-01
Erik Li
n
da
h
l
Fix gmx densit
y
for
non
-
mass calculatio
n
s
commit
|
commitdiff
|
tree
2017-12-28
David
v
an
d
er Spoel
F
ixes and u
p
dates for xplor2gml
.
p
l
and a
t
om_nom
.
tbl
commit
|
commitdiff
|
tree
2017-10-30
David v
a
n der Sp
o
el
Fixed mdp output from el
e
ctric field co
d
e
.
commit
|
commitdiff
|
tree
2017-10-27
Aleksei Iupinov
Remove
u
nu
s
ed PM
E
gr
i
d dump debug functio
n
s
commit
|
commitdiff
|
tree
2017-10-17
Davi
d
van der Spoel
Fixed
mi
s
sing entr
i
e
s in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-09-04
T
e
em
u
Mu
r
tola
Introduce
s
e
lf-pairs s
e
arch
in nb
s
earch
commit
|
commitdiff
|
tree
2017-09-04
Teemu Mur
t
ola
Ref
a
cto
r
analysis
n
b
search
t
ests
commit
|
commitdiff
|
tree
2017-08-09
Roland Schulz
Use table
E
wald for Skylake
commit
|
commitdiff
|
tree
2017-08-03
David van der Spoel
Fix
e
d bug in gmx d
i
s
res inde
x
i
n
g
array
s
.
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
M
a
ke loop
v
ariable
s
in orire
s
.
cpp local
commit
|
commitdiff
|
tree
2017-08-02
Berk
Hess
Ad
d
c
h
eck for nr o
f
orient
a
ti
o
n
restrain
t
s
commit
|
commitdiff
|
tree
2017-07-19
Davi
d
van der
Spo
e
l
Fixed test-order dependency in
g
mxpr
e
process te
s
ts
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
an d
e
r Spoe
l
F
ix non-reproducability of clustsi
z
e t
e
sts
.
commit
|
commitdiff
|
tree
2017-04-29
Carst
e
n
Kut
z
ne
r
Minor header fi
l
e cleanup in ED
,
IMD
a
nd CompEL modu
l
e
s
commit
|
commitdiff
|
tree
2017-04-22
Mark Abraham
Clean u
p
m
emor
y
usage with oenv
an
d
x
vg writi
n
g
commit
|
commitdiff
|
tree
2017-03-13
Teemu
M
urtola
Improve opt
i
o
n
s
upport
&
te
s
ts for key-value trees
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtola
R
emove
manual alig
n
ment from In
M
emorySerializer
commit
|
commitdiff
|
tree
2017-03-12
Teemu M
u
rtola
Con
s
ist
e
nt Te
x
t
Write
r
tra
i
ling whit
e
spa
c
e
h
andling
commit
|
commitdiff
|
tree
2017-03-12
David van der Spo
e
l
A
dde
d
tests for gmx clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
Vedran Mileti
ć
Document that we now
support A
M
D GCN on Mesa/
L
LVM
commit
|
commitdiff
|
tree
2017-02-28
Berk Hess
Add load balance fraction to DLB p
r
int
commit
|
commitdiff
|
tree
2017-02-28
T
eemu Mur
t
ola
More d
o
cumentation for key-
v
alue trees
commit
|
commitdiff
|
tree
2017-02-27
David
v
an
d
er Spo
e
l
Fix
e
s bu
g
in
gmx solv
a
te with
-shell that y
i
elded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-09
A
l
eksei Iupinov
A
dd initiali
z
ation to
dvdlambda in
bonded forces t
e
sts
commit
|
commitdiff
|
tree
2017-02-08
Mark
Abraha
m
Remove docs for unim
p
lemen
t
ed tr
j
conv -clus
t
ercenter
commit
|
commitdiff
|
tree
2017-02-02
Mark Abraham
Clar
i
f
y
use of
t
au-p
a
nd pcoupl
t
y
p
e
commit
|
commitdiff
|
tree
2017-01-30
Mark
Abraham
Don't print invalid
p
erf
o
rmance d
a
ta
commit
|
commitdiff
|
tree
2016-12-14
Mark Abraham
Fix mis
l
eading parallelization docs for gm
x
wha
m
commit
|
commitdiff
|
tree
2016-11-21
Aleksei
Iupino
v
Move hardco
d
ed PME g
r
id indexin
g
cons
t
ants into header
commit
|
commitdiff
|
tree
2016-11-18
David van der Spoe
l
Added first tests of bonded force
functi
o
ns
.
commit
|
commitdiff
|
tree
2016-11-16
Mark A
b
raham
Enhance
d
ArrayRef
commit
|
commitdiff
|
tree
2016-11-16
M
a
r
k
Abr
a
ham
C
reat
e
d
p
ad
d
edvec
t
or
.
h
commit
|
commitdiff
|
tree
2016-10-24
T
eemu Murtola
Electric field mdp parsing using options
commit
|
commitdiff
|
tree
2016-10-24
Teemu
M
urto
l
a
Support for def
a
ult values from Options to KeyValueTre
e
commit
|
commitdiff
|
tree
2016-10-14
Berk
H
ess
Apply Berendsen P-co
u
ple at n
s
tpco
u
ple step
s
commit
|
commitdiff
|
tree
2016-10-14
Teemu Murtola
Use gmx_mtop_t i
n
sel
e
ctions,
part 3
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Gett
e
r
for map
p
e
d
pa
t
hs
f
r
om
K
e
yVa
l
ueTreeTra
n
sf
o
rm
commit
|
commitdiff
|
tree
2016-10-08
Be
r
k He
s
s
A
dd
r
eadConf
A
ndTopology
commit
|
commitdiff
|
tree
2016-10-03
Philip
Lo
c
he
EW3DC for no
n
-neutral syst
e
ms
commit
|
commitdiff
|
tree
2016-10-01
Ber
k
Hess
Fix inputrec initia
l
i
z
ation
i
n 4 too
l
s
commit
|
commitdiff
|
tree
2016-09-29
Be
r
k H
e
ss
Use std::ve
c
tor in t_s
t
a
t
e
commit
|
commitdiff
|
tree
2016-09-29
Ber
k
Hess
Add flag
s
for
o
ptional t_ato
m
s entries
commit
|
commitdiff
|
tree
2016-09-20
Berk Hess
Remove state
d
uplication in serial runs
commit
|
commitdiff
|
tree
2016-09-20
D
avid van d
e
r S
p
oel
Made correla
t
ion functio
n
r
ou
t
ine
use
std::vecto
r
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Made distance re
s
traint
s
work with threads
a
nd
DD
commit
|
commitdiff
|
tree
2016-09-15
Alekse
i
I
upino
v
Mo
v
e the PME
Ewald coefficients to
t
he PME structure
commit
|
commitdiff
|
tree
2016-09-13
Roland Schulz
T
i
d
y: modernize-use-emplace
commit
|
commitdiff
|
tree
2016-09-13
Berk Hess
Change ED a
n
d s
w
apstate to pointe
r
s
in t_stat
e
commit
|
commitdiff
|
tree
2016-09-11
Ve
d
r
a
n
Miletić
Print OpenCL er
r
or
s
tring
i
nstead of error c
o
de
commit
|
commitdiff
|
tree
2016-09-10
Be
r
k Hess
R
e
m
o
ve
continua
t
ion
f
r
o
m conv
e
rt_tpr
commit
|
commitdiff
|
tree
2016-09-10
A
l
ek
s
ei Iupinov
Fix
P
ME data destructor no
t
being called
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Merge "Merge branch release-20
1
6"
commit
|
commitdiff
|
tree
2016-08-27
Szilárd Páll
M
a
ke
ASAN/TSAN/MSAN
build types easier t
o
discover
commit
|
commitdiff
|
tree
2016-08-27
Mark A
b
raha
m
Stop using
gm
x
_fa
t
al in
g
romp
p
commit
|
commitdiff
|
tree
2016-08-27
T
e
emu Murtola
Support KeyValu
e
Tree obj
e
cts in
refdat
a
commit
|
commitdiff
|
tree
2016-08-27
Be
r
k Hess
Reduce
r
ounding err
o
rs in SETTL
E
commit
|
commitdiff
|
tree
2016-08-27
R
o
lan
d
Schulz
Fix build wit
h
GMX
_
USE_TNG=off
commit
|
commitdiff
|
tree
2016-08-24
D
avid van
der Spo
e
l
Added documentation for shell pote
n
tials
.
commit
|
commitdiff
|
tree
2016-07-31
Da
v
id van der Spo
e
l
Merge "Merg
e
bra
n
ch release-5-1 into
r
elease-2
0
1
6
"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Vedran Milet
i
ć
Print
w
orking di
r
b
e
fore command li
n
e
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
Merge "Merge branch r
e
l
e
ase-
5
-1 into
r
elease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Szilárd Páll
User gui
d
e clarif
i
ca
t
i
o
ns
commit
|
commitdiff
|
tree
2016-07-07
Berk Hes
s
Rel
a
x
pull PBC
c
heck
commit
|
commitdiff
|
tree
2016-07-03
Berk
Hess
Ad
d
grompp chec
k
for
pull g
r
oup
commit
|
commitdiff
|
tree
2016-06-27
David van der
Spo
e
l
Made gm
x
dos work again
.
commit
|
commitdiff
|
tree
2016-06-26
Berk Hes
s
Fi
x
v
site bug
w
ith MPI+Op
e
nMP
commit
|
commitdiff
|
tree
2016-06-21
Berk He
s
s
Fix bug wit
h
f
bposres+MP
I
+OpenMP
commit
|
commitdiff
|
tree
2016-05-30
Berk Hes
s
Add
grompp
chec
k
for unbound atoms
commit
|
commitdiff
|
tree
2016-05-08
M
a
rk Abraham
Fix co
n
stants, units and con
v
er
s
ion factors
commit
|
commitdiff
|
tree
2016-03-23
D
a
vid
v
an der Spoel
Re
m
oved
sren
e
w
th
a
t was making array
s
maller incorrec
t
ly
.
commit
|
commitdiff
|
tree
2016-01-20
David van der S
p
oel
Couple
o
f ne
w
q
uotes
commit
|
commitdiff
|
tree
2015-12-09
Teemu Murtola
S
plit txtdump
.
*, part 1
commit
|
commitdiff
|
tree
2015-12-05
Magnus Lundbor
g
Wr
i
te forces a
n
d
v
elociti
e
s to
c
ompre
s
sed
T
N
G
.
commit
|
commitdiff
|
tree
2015-11-24
Dav
i
d van der Spoel
Fixes newly
introduced bug
in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
Dav
i
d van der
S
poel
Mo
v
ed domdec structures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David
van de
r
Spo
e
l
Clean
u
p
s
i
n le
g
acyheader/typ
e
s/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van d
e
r
Spoel
Merged
l
eg
a
c
y
hea
d
er
s
/types/q
m
mmr
e
c
.
h into
md
l
ib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Spoel
Mov
e
d legacyheader
s
/type
s
/grou
p
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van
de
r
Spoel
Merged legacyh
e
ade
r
s
/types/ns
.
h
and nblist
.
h t
o
mdty
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoel
Comb
i
ne
enums
.
h a
n
d n
a
mes*
.
commit
|
commitdiff
|
tree
2015-11-20
Mark Abraham
Split wallcycle
in
t
erface
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Mer
g
ed lega
c
yheaders/nrnb
.
h and typ
e
s
/n
r
nb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
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