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Update documention of Nose-Hoover output
2017-11-28
Berk He
s
s
Update documention of Nose-Hoover
o
utput
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Extend grompp
m
is
s
ing en
e
rgy ter
m
message
commit
|
commitdiff
|
tree
2017-11-10
Berk
Hes
s
Fi
x
genion charge summat
i
on a
c
curacy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add miss
i
n
g
Ewald
c
o
rrection for pme-user
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove inco
r
rect co
m
m
e
nt for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Ber
k
Hess
F
i
x gmx
c
heck for tprs with different
#atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix
i
ncorrect dV/dlambd
a
f
o
r walls
commit
|
commitdiff
|
tree
2017-10-20
B
e
rk
Hess
F
i
x w
a
r
n
i
n
g for c
o
nfout with periodi
c
molecu
l
es
commit
|
commitdiff
|
tree
2017-09-23
Ber
k
Hess
Fix
g
rompp w
i
th Andersen massive and no COM removal
commit
|
commitdiff
|
tree
2017-09-14
Ber
k
Hess
F
i
x nbnx
n
SIMD
2
xNN PME
t
abulated
k
e
rnel
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Fix exception in
S
IMD LJ P
M
E
solve
commit
|
commitdiff
|
tree
2017-09-11
Berk H
e
ss
Fix PBC bugs
i
n the
s
w
ap
code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hes
s
A
void i
n
f in
S
IMD doubl
e
sqrt()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
Fix FEP s
t
a
t
e wi
t
h re
r
un
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix orie
n
tat
i
on r
e
straint reference
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Add check f
o
r n
r
o
f
orientation res
t
rai
n
ts
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix bugs with orientat
i
on re
s
trai
n
ts
commit
|
commitdiff
|
tree
2017-06-12
Be
r
k Hess
Disa
b
le PME tuning wi
t
h the group sch
e
me
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Fi
x
n
ull pointer print i
n
D
D
commit
|
commitdiff
|
tree
2017-06-08
Berk Hess
F
ix COM pull
force wi
t
h SD
commit
|
commitdiff
|
tree
2017-06-02
Berk Hess
Fix initia
l
temperature
r
eporting
commit
|
commitdiff
|
tree
2017-05-15
Berk Hes
s
Fix LJPME + switch gr
o
mpp error
commit
|
commitdiff
|
tree
2017-05-14
Berk He
s
s
Fix b
u
gs in double Simd4 implementat
i
o
ns
commit
|
commitdiff
|
tree
2017-04-21
Be
r
k Hess
F
i
x bugs in d
o
u
ble AVX(2
)
_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Berk Hess
Fix
u
n
used SIMD P
M
E table kernel
commit
|
commitdiff
|
tree
2017-03-16
Berk Hes
s
Replace instance of group by coor
d
i
n
p
ull m
d
p docs
commit
|
commitdiff
|
tree
2017-02-07
Ber
k
H
e
s
s
Add mdp
o
pti
o
n
check with decoup
l
ed mod
e
s
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Reall
y
fix arra
y
o
f co
m
plex
in cro
s
s_corr
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Fix array of complex in cross_c
o
rr
commit
|
commitdiff
|
tree
2017-01-20
Berk Hess
Disallow overwriting o
f
di
h
edr
a
l ty
p
e 9
commit
|
commitdiff
|
tree
2017-01-17
Be
r
k Hess
Correct assert
o
n pm
e
-order
commit
|
commitdiff
|
tree
2017-01-05
Berk He
s
s
Fi
x
flat-bottom position re
s
traint
s
+ DD +
O
p
e
n
M
P
commit
|
commitdiff
|
tree
2016-12-14
Berk He
s
s
Add
b
onded #th
r
e
ad runtime che
c
k
commit
|
commitdiff
|
tree
2016-11-01
Berk Hes
s
F
i
x time label
print in gmx
v
anhov
e
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
D
L
B ca
n
n
ow
t
urn of
f
, when slower
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
Fix DLB
t
im
i
n
g
with
C
UDA and OpenCL
commit
|
commitdiff
|
tree
2016-10-12
B
er
k
He
s
s
Fixed print bug in gmx wham
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Fixed unused vari
a
bles in domdec
.
cp
p
commit
|
commitdiff
|
tree
2016-09-16
Ber
k
Hess
M
a
de di
s
tan
c
e res
t
raints
w
o
rk w
i
th threads and DD
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
F
ix
b
ug with conju
g
at
e
-
gra
d
ien
t
an
d
Ope
n
MP
commit
|
commitdiff
|
tree
2016-09-05
B
e
rk H
e
s
s
Re-e
n
a
ble flexible
cons
t
ra
i
nts w
i
t
h
DD
commit
|
commitdiff
|
tree
2016-09-02
Be
r
k Hess
Merge bra
n
c
h release-5
-
1
into
r
eleas
e
-2016
commit
|
commitdiff
|
tree
2016-09-02
B
er
k
Hess
Fix P
a
rrinell
o
-
R
a
hman with nstpcouple>1
commit
|
commitdiff
|
tree
2016-08-30
Berk H
e
ss
Make
viria
l
r
e
prod
u
c
ib
l
e
commit
|
commitdiff
|
tree
2016-08-24
Ber
k
Hess
Fix Ewald s
u
rface+
3
D
C
correctio
n
s
commit
|
commitdiff
|
tree
2016-08-24
Berk
H
e
s
s
M
e
rge
branch re
l
ea
s
e-5-1 into
r
elease-2016
commit
|
commitdiff
|
tree
2016-08-23
Berk Hes
s
R
e
mo
v
e var
i
a
b
le
p
recision gro writing
commit
|
commitdiff
|
tree
2016-08-17
Be
r
k Hess
F
i
xed opening of wall table files
commit
|
commitdiff
|
tree
2016-08-15
Ber
k
Hess
Redu
c
e
FE pair-
l
i
st mem
o
r
y us
a
ge
commit
|
commitdiff
|
tree
2016-08-10
Berk H
e
ss
Fix dea
d
lock with t
h
read-MPI
commit
|
commitdiff
|
tree
2016-08-09
Berk Hess
F
i
x
twin-cutoff for GPU LJ pot-switch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Relax pull PBC check
commit
|
commitdiff
|
tree
2016-07-05
Berk Hess
A
dd ch
e
cks for too much memory
in g_
n
meig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add
grompp
check
f
or pull group
commit
|
commitdiff
|
tree
2016-06-28
Berk He
s
s
Properly re
s
e
t
C
U
DA applicat
i
on clo
c
ks
commit
|
commitdiff
|
tree
2016-06-27
Berk H
e
ss
Use sy
s
conf(_S
C
_
NPRO
C
ESSORS_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
Berk
H
e
s
s
Fix vsite bug with MPI+O
p
en
M
P
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix Verlet
b
u
f
fer c
a
lculation
with n
s
tlis
t
=1
commit
|
commitdiff
|
tree
2016-06-23
Berk
H
ess
Mo
r
e accurate GPU list splitting
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Updated OpenCLTODOList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
A
d
d nbnxn pair-list
re
b
a
lancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Rem
o
v
e
O
penMP
ov
e
rhead
a
t
high para
l
lelization
commit
|
commitdiff
|
tree
2016-06-22
Berk H
e
ss
Correct GPU pair esti
m
ate for list splitting
commit
|
commitdiff
|
tree
2016-06-21
Be
r
k
H
ess
Fix bug
w
ith fbp
o
sres+M
P
I
+
OpenMP
commit
|
commitdiff
|
tree
2016-06-19
Ber
k
Hess
Remov
e
warnings on checkpoin
t
mism
a
tch
commit
|
commitdiff
|
tree
2016-06-17
Be
r
k Hess
R
e
mo
v
e st
d
::t
h
read::hardware_concurr
e
ncy()
commit
|
commitdiff
|
tree
2016-06-14
B
e
rk Hess
Fix OpenC
L
e
rror w
i
th empty domains
commit
|
commitdiff
|
tree
2016-06-13
Berk He
s
s
Handle
c
onstraint
errors with EM
commit
|
commitdiff
|
tree
2016-06-07
Ber
k
Hess
F
i
x data ra
c
e
i
n hwinfo wi
t
h thread-MP
I
commit
|
commitdiff
|
tree
2016-06-03
Berk He
s
s
Handle
partia
l
ly froz
e
n and c
o
nstrained atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Repo
s
ition nbnxn f
i
ller
pa
r
t
icles
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk Hess
Avoid numerica
l
overflow with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk
Hess
Add
c
heck for f
i
nite energies
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
Add gromp
p
check for un
b
o
un
d
atom
s
commit
|
commitdiff
|
tree
2016-05-23
Berk H
e
ss
F
i
x bug i
n
v
-rescale thermo
s
tat & r
e
plica exc
h
ange
commit
|
commitdiff
|
tree
2016-05-10
Berk
Hess
Optimiz
e
d
t
h
e
vsite threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Fix CUD
A
s
h
mem bug
commit
|
commitdiff
|
tree
2016-05-10
B
e
r
k
Hess
Suppor
t
cmap with QMMM
commit
|
commitdiff
|
tree
2016-05-08
Ber
k
Hess
U
p
da
t
e mdrun
term
i
n
a
tion i
n
fo
commit
|
commitdiff
|
tree
2016-05-06
B
erk H
e
ss
OpenMP
p
arallelizatio
n
for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
F
i
x p
u
ll
l
eg
e
nd with external p
o
te
n
tial
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Allow rc
o
u
lo
m
b>rvdw with PM
E
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
e
ss
Broadc
a
st pull ex
t
e
r
n
al
p
o
t
e
n
tial provi
d
er st
r
i
ng
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
Fi
x
g
m
x hbond group overlap check
commit
|
commitdiff
|
tree
2016-04-14
Berk Hes
s
Add QMMM check
s
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Correct nrdf for 1
D
/2D systems
commit
|
commitdiff
|
tree
2016-03-31
Ber
k
H
e
ss
Fix includes in readpu
l
l
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk
Hess
Add opt
i
on for
ext
e
rnal pu
l
l potential
commit
|
commitdiff
|
tree
2016-03-30
Berk
He
s
s
Correct mdrun tMPI (non-)parallel e
r
ror
mess
a
ge
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add
real
/
SIM
D
template
for L
J
-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk He
s
s
Avoid asserti
o
n failure
i
n pme_loa
d
bal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk
H
ess
M
a
ke gmx van
h
ove wo
r
k without PBC
commit
|
commitdiff
|
tree
2016-03-22
B
erk H
e
ss
LJ combination
r
ule ker
n
els for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Berk Hess
Moved
p
ull initialization back t
o
m
drunner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix no
n
-normalization of FFT au
t
oc
o
rr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Re
m
ove restriction on
d
ihdral
t
ypes or
d
er
commit
|
commitdiff
|
tree
2016-03-12
Berk
Hess
Split off Fermi kern
e
l fro
m
CUDA
k
erne
l
commit
|
commitdiff
|
tree
2016-03-09
B
erk Hes
s
F
i
x Ewald 3DC dipol
e
with Verle
t
scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
Converted csettl
e
() to use re
a
l/
S
imdRea
l
t
em
p
la
t
e
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use SIMD transpose scatter in bonded
s
commit
|
commitdiff
|
tree
next