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Update documention of Nose-Hoover output
2017-11-28
Berk Hess
Update do
c
umention of Nose-Hoover
o
u
tput
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hess
Extend grompp mis
s
ing energy term mess
a
ge
commit
|
commitdiff
|
tree
2017-11-10
Berk He
s
s
Fi
x
g
e
ni
o
n
c
h
a
rge summation accuracy
commit
|
commitdiff
|
tree
2017-11-02
B
e
rk
Hess
Add miss
i
ng Ewald correct
i
on for pme-use
r
commit
|
commitdiff
|
tree
2017-10-29
B
e
rk Hess
Re
m
ove in
c
orrect comment for CHARMM tips3
p
commit
|
commitdiff
|
tree
2017-10-24
Be
r
k Hess
Fix gmx check
f
o
r t
p
rs
w
ith different
#atom
s
commit
|
commitdiff
|
tree
2017-10-23
B
erk Hess
Fix incorrect dV/dlambda for wal
l
s
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning for confout with pe
r
i
o
dic mo
l
ecules
commit
|
commitdiff
|
tree
2017-09-23
Ber
k
Hess
Fix gro
m
p
p
with An
d
er
s
en massive and no
C
O
M removal
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix nbnxn SIMD 2xNN PM
E
t
abul
a
ted
kernel
commit
|
commitdiff
|
tree
2017-09-12
Berk
H
e
s
s
F
ix
e
xception in SIMD LJ P
M
E solve
commit
|
commitdiff
|
tree
2017-09-11
Berk
H
ess
Fix P
B
C bugs in the swap code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avoid inf in SIMD
double sqr
t
()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
Fix FEP state with rerun
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
F
ix ori
e
ntati
o
n res
t
r
a
i
nt
r
efe
r
ence
commit
|
commitdiff
|
tree
2017-08-03
B
e
r
k H
e
ss
A
d
d check for nr of ori
e
ntati
o
n restra
i
nts
commit
|
commitdiff
|
tree
2017-08-03
B
erk Hess
Fi
x
bugs w
i
th orientat
i
o
n restraints
commit
|
commitdiff
|
tree
2017-06-12
Berk
H
ess
Disable
PME tuning
w
ith t
h
e group
s
ch
e
me
commit
|
commitdiff
|
tree
2017-06-12
Berk H
e
ss
Fi
x
n
ull pointer
prin
t
i
n DD
commit
|
commitdiff
|
tree
2017-06-08
Berk He
s
s
Fix COM pull
f
o
rce with SD
commit
|
commitdiff
|
tree
2017-06-02
Berk Hess
Fix initia
l
tem
p
erature reporting
commit
|
commitdiff
|
tree
2017-05-15
Berk Hess
Fix
L
JPME + switch
g
rompp error
commit
|
commitdiff
|
tree
2017-05-14
Berk Hess
Fix
bugs in d
o
uble
Simd4 implementations
commit
|
commitdiff
|
tree
2017-04-21
Berk H
e
ss
Fix bugs in double
AVX(2
)
_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Berk Hess
Fix unused SIM
D
PME tabl
e
kernel
commit
|
commitdiff
|
tree
2017-03-16
Berk Hes
s
Repl
a
ce instance of
g
r
o
u
p
b
y c
o
ord in pull mdp docs
commit
|
commitdiff
|
tree
2017-02-07
Berk Hess
Add mdp optio
n
c
he
c
k w
i
th
d
ecoupled m
o
des
commit
|
commitdiff
|
tree
2017-02-02
B
er
k
Hess
Real
l
y fix arr
a
y of c
o
mplex in
c
r
o
ss_corr
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Fix
array of c
o
mplex in cross_corr
commit
|
commitdiff
|
tree
2017-01-20
Be
r
k Hess
D
i
sallow overw
r
itin
g
of
d
ihedral
t
y
pe 9
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Correct a
s
sert on pme-
o
rde
r
commit
|
commitdiff
|
tree
2017-01-05
Berk Hess
Fix flat-
b
ottom position
r
estraints
+ DD +
O
pe
n
MP
commit
|
commitdiff
|
tree
2016-12-14
Berk
H
ess
Add bonded
#thread
runtime check
commit
|
commitdiff
|
tree
2016-11-01
Berk
H
ess
Fix time label print i
n
gmx vanhov
e
commit
|
commitdiff
|
tree
2016-10-28
Berk Hes
s
DLB can no
w
turn off, when s
l
ow
e
r
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
Fix DLB timing with CUDA and Ope
n
CL
commit
|
commitdiff
|
tree
2016-10-12
Berk H
e
ss
Fixed
print bug in gmx wham
commit
|
commitdiff
|
tree
2016-09-16
Berk H
e
ss
Fixed unused v
a
ri
a
bles in d
o
m
d
ec
.
cpp
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
M
ade distance restr
a
ints
w
ork with thr
e
ads
a
nd
D
D
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
Fix
b
u
g
with
co
n
jugat
e
-gradient
and OpenMP
commit
|
commitdiff
|
tree
2016-09-05
Berk He
s
s
Re-enable
flexible constraints with DD
commit
|
commitdiff
|
tree
2016-09-02
B
e
rk Hess
Merge br
a
nch r
e
lease-5-
1
into release-2016
commit
|
commitdiff
|
tree
2016-09-02
B
e
rk H
e
ss
Fix Parrinel
l
o-Rahman w
i
th ns
t
pcouple>1
commit
|
commitdiff
|
tree
2016-08-30
Berk Hes
s
Make virial reprodu
c
ible
commit
|
commitdiff
|
tree
2016-08-24
Be
r
k Hess
Fix
E
wald
su
r
f
a
c
e+3DC corrections
commit
|
commitdiff
|
tree
2016-08-24
Berk Hes
s
Merge bran
c
h releas
e
-5-1 into
release-
2
016
commit
|
commitdiff
|
tree
2016-08-23
B
erk He
s
s
R
emove variable precision gro
w
r
itin
g
commit
|
commitdiff
|
tree
2016-08-17
Berk Hess
Fi
x
ed opening of wal
l
t
a
ble files
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
Reduce FE
pair-l
i
st
memory u
s
age
commit
|
commitdiff
|
tree
2016-08-10
B
e
r
k
Hess
F
i
x deadl
o
ck with thre
a
d-MPI
commit
|
commitdiff
|
tree
2016-08-09
B
e
rk Hess
Fi
x
twin-cutof
f
for GP
U
LJ pot-switch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Rel
a
x pull PBC check
commit
|
commitdiff
|
tree
2016-07-05
Ber
k
Hes
s
Add
checks for
t
oo much memory in g_nme
i
g
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add grompp c
h
eck for p
u
l
l
group
commit
|
commitdiff
|
tree
2016-06-28
B
erk Hess
Properly reset
CU
D
A application clocks
commit
|
commitdiff
|
tree
2016-06-27
Berk
H
ess
Use
sysconf(
_
S
C
_NPROCESS
O
RS_
O
NLN)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix vsite bug with MPI
+
OpenMP
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix Verl
e
t
buffer c
a
lculation w
i
t
h
ns
t
list=1
commit
|
commitdiff
|
tree
2016-06-23
B
e
rk Hess
More accurate GPU
lis
t
spl
i
tting
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
ess
Updated OpenCLTO
D
OLis
t
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Ber
k
He
s
s
Add nb
n
xn pair-
l
i
st rebalancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove OpenMP overhead
a
t high parallelization
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
e
ss
Corr
e
ct G
P
U pa
i
r estimate fo
r
l
i
s
t
splitting
commit
|
commitdiff
|
tree
2016-06-21
Berk
H
ess
F
i
x bug w
i
th f
b
po
s
res+MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
R
e
move warnings on checkpoint mismat
c
h
commit
|
commitdiff
|
tree
2016-06-17
B
erk
Hess
Remove
s
t
d::thr
e
ad::har
d
wa
r
e_co
n
currency()
commit
|
commitdiff
|
tree
2016-06-14
Ber
k
Hess
Fix Op
e
nCL err
o
r with empty doma
i
ns
commit
|
commitdiff
|
tree
2016-06-13
Berk Hess
Handle c
o
nstraint errors
with EM
commit
|
commitdiff
|
tree
2016-06-07
Berk
H
ess
Fix
data rac
e
i
n
hw
i
nfo wi
t
h thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
Be
r
k Hes
s
Hand
l
e par
t
ially frozen
and constrai
n
ed atoms
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk
H
e
ss
Reposition
nbnxn f
i
ller partic
l
es
commit
|
commitdiff
|
tree
2016-05-31
Ber
k
H
ess
Avoid
n
umer
i
cal
o
ver
f
l
o
w with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk
H
e
ss
Add
check for finite
ener
g
ies
commit
|
commitdiff
|
tree
2016-05-30
Berk He
s
s
Add grom
p
p check for unbound ato
m
s
commit
|
commitdiff
|
tree
2016-05-23
Berk
H
es
s
Fix bug in v-res
c
ale thermostat & replica exchange
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
O
p
ti
m
i
zed t
h
e v
s
ite threadin
g
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk Hess
F
i
x CU
D
A shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Support cmap with QMMM
commit
|
commitdiff
|
tree
2016-05-08
B
e
r
k Hess
Update mdrun termination
i
n
fo
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
O
penMP parallelization for pu
l
l
commit
|
commitdiff
|
tree
2016-04-20
B
e
rk H
e
ss
Fix pull legend with
e
x
ternal
potential
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>rvdw with PME
commit
|
commitdiff
|
tree
2016-04-19
Be
r
k H
e
ss
Broadcast pul
l
external potential
p
rovi
d
e
r
string
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
Fix gmx hb
o
nd group
o
ve
r
lap check
commit
|
commitdiff
|
tree
2016-04-14
Berk H
e
ss
Add QMMM checks
commit
|
commitdiff
|
tree
2016-04-03
Berk
H
ess
Corre
c
t n
r
df for 1D/2D
s
y
stem
s
commit
|
commitdiff
|
tree
2016-03-31
B
erk Hess
Fix inc
l
u
d
es in
read
p
ul
l
.
c
p
p
commit
|
commitdiff
|
tree
2016-03-31
Ber
k
Hess
Add o
p
tion for e
x
ternal
p
ull poten
t
ial
commit
|
commitdiff
|
tree
2016-03-30
Berk He
s
s
Correct
m
dr
u
n tMPI (non-)para
l
l
e
l error m
e
s
s
a
g
e
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add real/SIMD
templ
a
te for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
A
v
oid assertion fai
l
ure in pme_loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
B
erk Hes
s
Make gmx
v
a
nhove
w
ork without PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combination rule
kernels for CUD
A
commit
|
commitdiff
|
tree
2016-03-21
Berk Hes
s
M
oved
p
ull initialization back to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
B
e
rk H
e
ss
F
i
x non-
n
or
m
alizat
i
on of FFT au
t
o
c
orr
commit
|
commitdiff
|
tree
2016-03-14
Berk
Hes
s
Re
m
ove restriction on d
i
hdraltyp
e
s or
d
er
commit
|
commitdiff
|
tree
2016-03-12
Ber
k
Hes
s
Split off Ferm
i
kern
e
l from
C
UDA
k
ernel
commit
|
commitdiff
|
tree
2016-03-09
Ber
k
Hess
Fix Ewa
l
d 3DC di
p
ole with
Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
B
erk Hess
Converted c
s
ett
l
e() to
use real/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use SIMD transpose scatter in bo
n
d
e
ds
commit
|
commitdiff
|
tree
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