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Add grompp check for unbound atoms
2016-05-30
Berk Hess
A
dd
g
r
ompp check for unbound atoms
commit
|
commitdiff
|
tree
2016-05-23
Berk Hes
s
Fix
bug in v-resc
a
le thermostat &
r
e
p
lica exc
h
ange
commit
|
commitdiff
|
tree
2016-05-10
Berk H
e
ss
O
p
timiz
e
d the vsite threading
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk H
e
ss
Fix CUDA shm
e
m b
u
g
commit
|
commitdiff
|
tree
2016-05-10
Berk He
s
s
Support cmap with QMMM
commit
|
commitdiff
|
tree
2016-05-08
Ber
k
Hess
U
p
d
a
te mdr
u
n ter
m
in
a
tion info
commit
|
commitdiff
|
tree
2016-05-06
B
e
rk
H
ess
Ope
n
MP paral
l
elization
for
p
ul
l
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pull legen
d
with external pot
e
ntial
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>rv
d
w
w
ith PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
B
r
o
a
d
cas
t
pull external po
t
ential p
r
ovider string
commit
|
commitdiff
|
tree
2016-04-19
Ber
k
Hess
Fix
g
mx hb
o
nd group
o
verlap che
c
k
commit
|
commitdiff
|
tree
2016-04-14
Berk Hess
Add Q
M
MM checks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hes
s
Correct nr
d
f for 1D/2D system
s
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix includes
in readpull
.
c
pp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
A
dd opt
i
on fo
r
external pull potential
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct mdrun
t
MPI
(
non-)pa
r
a
l
lel error message
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add real/SIMD t
e
mplate for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoid assertio
n
failure
in pme_l
o
adbal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Make gmx vanhove
w
ork w
i
thout
P
BC
commit
|
commitdiff
|
tree
2016-03-22
Berk
H
ess
LJ combination r
u
le
k
ernels
for CUD
A
commit
|
commitdiff
|
tree
2016-03-21
Berk Hess
Moved pull
i
n
itial
i
zation
back to mdru
n
ner
commit
|
commitdiff
|
tree
2016-03-18
B
e
rk
H
ess
Fix non-normalizatio
n
of
FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove r
e
striction on dihdral
t
yp
e
s order
commit
|
commitdiff
|
tree
2016-03-12
B
e
r
k
Hess
Split off Fermi
k
ernel from CUDA ke
r
nel
commit
|
commitdiff
|
tree
2016-03-09
Ber
k
He
s
s
Fix
E
wald 3DC dipo
l
e with Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk Hes
s
Convert
e
d csettle() t
o
use real/Simd
R
eal templ
a
te
commit
|
commitdiff
|
tree
2016-03-03
Ber
k
Hess
U
se S
I
MD tr
a
nspose
scatte
r
in bond
e
d
s
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
s
e rvec4 for listed for
c
e buff
e
r
commit
|
commitdiff
|
tree
2016-02-27
Berk Hes
s
R
e
mo
v
e
epsf
a
c from GPU kernel
inner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Minor code r
e
orde
r
in
g
in GPU ke
r
ne
l
s
commit
|
commitdiff
|
tree
2016-02-26
Berk He
s
s
Fix compilation with Simd
4
F
loat, without Simd4
D
ouble
commit
|
commitdiff
|
tree
2016-02-19
Berk Hess
Fix excess
i
ve list splitt
i
ng
commit
|
commitdiff
|
tree
2016-02-17
Berk He
s
s
R
en
a
m
e
d nbnxn st
a
tic con
s
t
ints
commit
|
commitdiff
|
tree
2016-02-11
Berk
Hess
A
d
d SIMD version of
pbc_
d
x_aiu
c
commit
|
commitdiff
|
tree
2016-02-09
Berk Hess
Repl
a
ced nbnxn sea
r
ch+grid simd macros
commit
|
commitdiff
|
tree
2016-02-07
B
e
r
k
Hess
Fix
inc
o
rrect cmap parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk He
s
s
F
i
x
i
ncorrect cmap parsi
n
g
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
R
epl
a
ced
literals in nbnxn lists by int
s
commit
|
commitdiff
|
tree
2016-02-03
Berk
H
e
ss
F
i
x
m
drun removing
V
erlet buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix SET
T
LE
e
r
ror h
a
ndling
commit
|
commitdiff
|
tree
2016-01-29
B
e
r
k Hess
Added d
o
cumenta
t
io
n
for pme grid indexin
g
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI ignorin
g
P
M
E mesh contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk He
s
s
Update
-ntomp_pme -n
p
me
c
he
c
k
commit
|
commitdiff
|
tree
2016-01-29
Berk
Hess
Ad
d
c
h
eck for double per
t
urbatio
n
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix LINCS tria
n
gle con
s
tra
i
n
t threa
d
issue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Update pair-list bu
f
fer manual
commit
|
commitdiff
|
tree
2016-01-24
B
erk H
e
ss
Fi
x
exact
c
ontinuation fro
m
n
o
n-energy s
t
eps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fi
x
energ
y
file continuat
i
on w
i
th md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
F
i
x
energy a
v
erag
e
with c
o
ntin
u
ation
commit
|
commitdiff
|
tree
2016-01-08
Berk
H
ess
Fix P
M
E load balancing skipp
i
ng a setup
commit
|
commitdiff
|
tree
2015-12-29
Berk He
s
s
C
or
r
ec
t
vector check of gm
x
check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorganized domdec initial
i
z
ation
commit
|
commitdiff
|
tree
2015-12-20
B
erk He
s
s
Merge release
-
5
-
1 into
master
commit
|
commitdiff
|
tree
2015-12-19
Be
r
k He
s
s
Brin
g
performance es
t
imation
u
p to date
commit
|
commitdiff
|
tree
2015-12-17
Be
r
k Hess
Removed to
p
ology poin
t
ers
f
r
o
m D
D
struc
t
commit
|
commitdiff
|
tree
2015-12-16
Berk H
e
ss
Add
one e
l
emen
t
t
o state rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
R
emov
e
d u
n
u
s
ed mdrun option -dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hes
s
Fix bug with pull group wei
g
hts
commit
|
commitdiff
|
tree
2015-12-07
Berk Hess
Moved pull params to mdtypes/pull-param
s
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Increase pdb c
h
ain
i
d
s
t
o 62 in outpu
t
commit
|
commitdiff
|
tree
2015-12-02
Ber
k
Hess
Refactored
s
e
t_pbc_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk
H
ess
Made
t
_i
n
putrec con
s
t in PME
loa
d
b
a
lancing
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pull group count for coo
r
ds st
o
r
ed in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
Re
m
o
v
e
d
mdrun fatal_
e
rror with P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
Be
r
k Hess
Removed Reactio
n
-F
i
eld-ne
c
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Opti
m
ized t
h
e
bonded
t
h
read force re
d
uctio
n
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fix
e
d
(harmless)
f
p excep
t
ion
i
n wallcycl
e
_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk
H
ess
Cor
r
ect L
I
NCS dHdl contribu
t
ion
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Fix no wallc
y
cle
support
commit
|
commitdiff
|
tree
2015-11-03
Berk
H
ess
Rem
o
ved n
b
nxn kerne
l
blendv op
t
imizati
o
n
commit
|
commitdiff
|
tree
2015-11-02
B
e
r
k
Hess
Fix
inter
m
olecular interactions with small mols
commit
|
commitdiff
|
tree
2015-10-15
Be
r
k Hess
F
i
x
e
d nbnxn_4xN
p
erformanc
e
regression
commit
|
commitdiff
|
tree
2015-10-07
Berk
H
ess
F
ix bu
g
s with i
n
term
o
l interactions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
R
e
moved CUD
A
polling
wait
commit
|
commitdiff
|
tree
2015-09-27
Berk Hes
s
Mo
v
e gmx_domd
e
c_comm_t d
e
f
i
nition
commit
|
commitdiff
|
tree
2015-09-22
Berk H
e
ss
R
e
mo
v
e
d
u
s
eless mu
l
tiple s
h
i
f
ts
i
n
p
b
c
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
Split nbnxn_grid
.
c
o
f
f
f
ro
m
nbnxn_search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
Detect
i
n
correct
c
ycle counting
commit
|
commitdiff
|
tree
2015-08-25
Berk Hess
Si
m
p
l
ify changing
t
he
t
px_v
e
rsion
commit
|
commitdiff
|
tree
2015-08-14
Berk
H
e
s
s
Make mdrun
-nt w
o
rk aga
i
n
commit
|
commitdiff
|
tree
2015-08-13
Berk Hess
Added se
t
_pull_coo
r
d_reference_value
commit
|
commitdiff
|
tree
2015-08-12
B
erk
H
ess
Added const qualifiers to cor
e
MD routines
commit
|
commitdiff
|
tree
2015-07-08
Berk Hess
Se
p
a
rated bonded and
E
wald correction t
h
reading
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
F
i
x
too
s
mal
l
GP
U
pair coun
t
estimates
commit
|
commitdiff
|
tree
2015-07-06
B
er
k
He
s
s
Fix
b
ug in GPU li
s
t
balan
c
ing
commit
|
commitdiff
|
tree
2015-07-05
Berk
H
ess
Fix DD DLB
state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix bug in GPU list balancing
commit
|
commitdiff
|
tree
2015-07-04
B
e
rk He
s
s
Obey Open
M
P
t
hr
e
a
d
count limi
t
wit
h
tMPI
commit
|
commitdiff
|
tree
2015-07-04
Ber
k
Hess
Fix two PME DLB trigger issues
commit
|
commitdiff
|
tree
2015-07-03
Berk Hess
Correct gro
m
pp pull
w
arning mes
s
age
commit
|
commitdiff
|
tree
2015-06-30
Berk H
e
ss
Fix incon
s
istent OpenM
P
automation
commit
|
commitdiff
|
tree
2015-06-30
B
er
k
Hess
e
nabled
1
PP + 1 PME nod
e
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add c
h
ecks for in
e
f
f
icient resource usage
commit
|
commitdiff
|
tree
2015-06-29
B
e
rk Hess
Imp
r
ove DLB+PME
tuning
with GPUs
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Im
p
rove pair search thread load b
a
la
n
ce
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improved the intra-GPU load
balan
c
ing
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Reduce the use of nbnxn_
c
on
s
ts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
C
o
rrected nstcalclr/nstfep/n
s
t_repl_e
x
c
h
e
c
ks
commit
|
commitdiff
|
tree
2015-06-26
Berk Hess
F
ixed
V
erlet b
u
ffer issue
w
ith
2
-wide
SIMD
commit
|
commitdiff
|
tree
2015-06-25
Berk
Hess
Intermolecular
bonded interaction
suppor
t
added
commit
|
commitdiff
|
tree
next