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Add tip4pew parameters to oplsaa.ff
2015-01-15
Berk Hess
Fix allocation issue with VV integra
t
or
commit
|
commitdiff
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tree
2014-12-22
Berk H
e
ss
Fixed p
b
c=xy
+
2 walls + Verlet scheme
commit
|
commitdiff
|
tree
2014-12-22
Be
r
k He
s
s
Fix bug F
E
+
GPU + 2/3D domain de
c
omposition
commit
|
commitdiff
|
tree
2014-12-11
B
e
r
k Hess
Adde
d
grompp error
for pulling to negative distance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix recent bug with trilinic
1
D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hes
s
Fixed pull co
o
rd
i
nit with rate!=0,
t_start
!
=0
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Ad
d
ed P
B
C
note to com
m
-mod
e
=
angular warning
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
M
ake dom
d
ec a p
r
o
pe
r
module
commit
|
commitdiff
|
tree
2014-12-05
Berk He
s
s
Clarified grom
p
p pull er
r
o
r
me
s
sages
commit
|
commitdiff
|
tree
2014-12-05
Berk
Hess
Avoid race on d
v
d
l w
i
th V
e
r
l
et+
O
penMP+LIN
C
S+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
A
dded
w
arning for unneces
s
a
ry s
o
ft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
F
i
x
e
d triclinic 1xNx1 dom
a
in dec
o
mp
o
sition
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
Fixed twin-range
+
f
reeze + constrai
n
ts
commit
|
commitdiff
|
tree
2014-11-24
Berk Hess
Avoid
N
aN i
n
rlist buffer ca
l
culation
commit
|
commitdiff
|
tree
2014-11-12
B
erk Hess
Corrected parameter for s
o
r
ti
n
g
on search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Fix DD b
o
n
d
ed interaction range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Rem
o
v
e
d f_novirsum reductio
n
in
V
erlet scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
F
ix
e
s iss
u
e with vsiten and Verlet buffers
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
A
v
oid DLB with o
v
erloaded P
M
E
r
anks
commit
|
commitdiff
|
tree
2014-09-30
Be
r
k Hess
Added G
P
U local wait to load bal
a
nci
n
g
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
ess
Dom
a
in decomposition now checks t
h
e rlist buffer
commit
|
commitdiff
|
tree
2014-09-29
Berk He
s
s
SIMD acceleration for
RB dihedrals
commit
|
commitdiff
|
tree
2014-09-29
Berk H
e
s
s
Avo
i
d PME tuning de
c
reasing rcoulo
m
b
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
F
i
x
c
alc_
g
r
i
d
a
v
oiding PME grid factor
8
4
commit
|
commitdiff
|
tree
2014-09-09
Be
r
k Hess
Fixed DD state
collection issue
commit
|
commitdiff
|
tree
2014-09-08
B
erk Hess
Chec
k
for im
p
licit
solven
t
+ Verl
e
t
scheme
commit
|
commitdiff
|
tree
2014-08-28
B
erk Hess
Fix
e
d t
w
o PME issues
w
ith MPI+
O
penMP
commit
|
commitdiff
|
tree
2014-08-25
Be
r
k Hess
Fixed bug
s
in
v
s
i
teN w
i
th OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk He
s
s
Initialize
unused velocity
c
o
n
s
t
r
a
int components
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
Halved the
c
o
s
t of the p
u
ll
co
m
m
unication
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Corrected SIMD math
overflow documentation
commit
|
commitdiff
|
tree
2014-08-10
B
erk
H
ess
Added checks fo
r
TPI + Verlet
scheme
commit
|
commitdiff
|
tree
2014-08-05
Berk Hess
Fix hang with LJ-PME and
e
mpty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
Fix
e
d PM
E
b
u
g
with high OpenMP t
h
rea
d
count
commit
|
commitdiff
|
tree
2014-07-31
B
erk Hess
Avoi
d
d
ivi
s
i
o
n by 0 in nbnxn_
s
earch
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
T
ake LJ-PME into
a
cc
o
u
n
t
f
or table
sp
a
cing
commit
|
commitdiff
|
tree
2014-06-29
Berk
Hess
Updated LJ
-
P
ME documentation
commit
|
commitdiff
|
tree
2014-06-24
Be
r
k Hess
Fix
e
d
the sign of mass
p
erturbed contribution
commit
|
commitdiff
|
tree
2014-06-20
B
e
rk Hess
Fix g_mindist with pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Ber
k
Hess
Fixed shells with particle d
e
co
m
posi
t
i
o
n
commit
|
commitdiff
|
tree
2014-06-18
Berk He
s
s
Fixed
sign error in posre
s
dvdl
commit
|
commitdiff
|
tree
2014-06-17
Berk He
s
s
Upd
a
t
ed mdrun -npme docu
m
entation
commit
|
commitdiff
|
tree
2014-06-17
Berk H
e
ss
Removed ro
u
nding iss
u
e
i
n nbn
x
n Ewald table
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
Fix
e
d PME bug wi
t
h
#OpenMP
-
t
hrea
d
s a
l
a
rge prime
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Chan
g
e
d
a
ppending file
n
ame
e
rror message
commit
|
commitdiff
|
tree
2014-06-13
Berk
Hess
Mad
e
sh
e
lls work with the V
e
rlet
schem
e
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
F
ixe
d
perturbe
d
wa
l
l
i
nteract
i
ons
commit
|
commitdiff
|
tree
2014-06-12
Berk He
s
s
Made gmxcheck -rms
d
work
again wit
h
forces
commit
|
commitdiff
|
tree
2014-06-11
Be
r
k Hess
Decouple
d
rep
l
_
e
x_nst from nstca
l
c
e
nergy
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Made repl_e
x
time step mo
r
e re
a
dable
commit
|
commitdiff
|
tree
2014-06-10
Berk Hess
Replaced gmx_hostname_num by gmx_phy
s
ical
n
ode_i
d
_hash
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
S
et
m
ake_ndx max na
m
e l
e
ngth and count to
1
0
24
commit
|
commitdiff
|
tree
2014-06-05
Berk Hes
s
Fixed shift and switch modifie
r
s
, par
t
icularly
for
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
B
e
rk
Hess
Fix
c
o
nstraint v
i
ria
l
with
m
ultiple time steppi
n
g
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed
g_energ
y
Eins
t
ein viscosi
t
y
commit
|
commitdiff
|
tree
2014-05-22
B
erk Hess
Avo
i
d ener
g
y
dri
f
t
w
i
th v
e
rlet-
b
uffer-tolera
n
c
e
commit
|
commitdiff
|
tree
2014-05-09
Ber
k
Hess
Minor tweaks to the DD setup
commit
|
commitdiff
|
tree
2014-04-29
Berk H
e
ss
Rem
o
ved truncation of nrd
f
in v-
r
e
s
cale thermos
t
at
commit
|
commitdiff
|
tree
2014-04-23
Berk
H
ess
Fix
e
d
n
bnxn FE list a
l
l
ocati
o
n issue
commit
|
commitdiff
|
tree
2014-04-02
Berk Hess
Add
e
d
L
J-PM
E
and LJ Pot-switch t
o
PME load estimate
commit
|
commitdiff
|
tree
2014-03-24
Berk Hes
s
A
d
ds
c
ut-off c
h
ecks
f
o
r triclinic domain decom
p
osit
i
on
commit
|
commitdiff
|
tree
2014-03-23
Berk
H
ess
F
i
xe
d
bug in p
a
ral
l
el v/f constraining
commit
|
commitdiff
|
tree
2014-03-23
Ber
k
Hess
CUDA cut-off kernels
no
w
shift exclusion e
n
ergi
e
s
commit
|
commitdiff
|
tree
2014-03-11
B
e
rk Hess
PME lo
a
d balancing
now wor
k
s with LJ-PME
commit
|
commitdiff
|
tree
2014-03-06
B
e
rk Hess
Fixed exit wi
t
h FEP with PME
nodes with
o
ut LJ-P
M
E
commit
|
commitdiff
|
tree
2014-03-05
Berk
H
ess
Buffer est
i
mate now works with rvd-s
w
itch=0
commit
|
commitdiff
|
tree
2014-02-26
Berk Hess
Free-
e
nergy now works
w
ith
t
he Verl
e
t scheme
commit
|
commitdiff
|
tree
2014-02-25
B
e
r
k Hess
Fix
e
s seperate PME no
d
es without
L
J-PME
commit
|
commitdiff
|
tree
2014-02-24
Be
r
k
H
e
ss
Im
p
lem
e
n
t
e
d L
J
-PME nbnxn kerne
l
s
commit
|
commitdiff
|
tree
2014-02-24
Ber
k
Hess
Fixed bug with LJ pot-switch in
4
xN kernels
commit
|
commitdiff
|
tree
2014-02-19
Berk Hess
Implemented nbnxn LJ switch functio
n
s
commit
|
commitdiff
|
tree
2014-01-30
Berk He
s
s
Made reference SIMD wor
k
a
gain
commit
|
commitdiff
|
tree
2014-01-29
Berk He
s
s
Au
t
omated Verlet
rlist f
o
r NVE simul
a
t
ions
commit
|
commitdiff
|
tree
2013-12-03
B
e
r
k H
e
ss
R
e
moved re
s
trictio
n
of on
e
r
eference pul
l
group
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Made cutoff-scheme=Verlet the default
commit
|
commitdiff
|
tree
2013-12-02
Berk
Hess
R
e
na
m
ed verlet-bu
f
fer-
d
rift to verlet-b
u
ffer-toler
a
nc
e
commit
|
commitdiff
|
tree
2013-12-01
Berk Hess
Fixe
d
zero hard
w
are
thread
count
commit
|
commitdiff
|
tree
2013-11-29
B
erk Hess
Created SI
M
D module
commit
|
commitdiff
|
tree
2013-11-26
B
erk
He
s
s
Fixed ret
u
rn val
u
e of
g
mx_mtop_
b
o
ndeds_free_energy
commit
|
commitdiff
|
tree
2013-11-15
Berk
H
ess
corre
c
te
d
pot
e
ntial nbnxn
S
I
MD memory issue
commit
|
commitdiff
|
tree
2013-11-08
B
e
rk
H
ess
fix nbnx
n
atom s
o
rting with d
i
stant bondeds
commit
|
commitdiff
|
tree
2013-11-07
Berk H
e
ss
corrected dynamic lo
a
d balancing when s
h
a
ring
GPUs
commit
|
commitdiff
|
tree
2013-11-05
Be
r
k Hes
s
G
PU detection is done o
n
ce per physi
c
al
n
ode
commit
|
commitdiff
|
tree
2013-11-05
B
e
rk Hess
r
emoved (harmless) left-over in nbnxn
SIMD kern
e
l
s
commit
|
commitdiff
|
tree
2013-10-31
B
e
rk Hes
s
reorgani
z
ed GP
U
de
t
ecti
o
n and selection
commit
|
commitdiff
|
tree
2013-10-29
Be
r
k
H
e
s
s
cor
r
ected
vo
l
um
e
with serial NPT replica e
x
change
commit
|
commitdiff
|
tree
2013-10-28
Berk Hess
i
m
proved the n
b
nxn buffer size es
t
imate with GPUs
commit
|
commitdiff
|
tree
2013-10-22
B
erk H
e
ss
fixed
rece
n
t
b
ug with CUDA texture ob
j
ects
commit
|
commitdiff
|
tree
2013-10-22
B
e
rk Hess
fixe
d
Ope
n
MP threads
being pinned to
the
same cores
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
avoi
d
d
i
vision by z
e
ro in SIM
D
ang
l
es
a
nd dihedr
a
ls
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
fixed a
h
alf bin
m
is
a
l
ignment in
g
mx_van
h
o
ve -or
commit
|
commitdiff
|
tree
2013-10-11
Berk H
e
s
s
i
ntr
o
duced general 4-wide S
I
MD
s
uppo
r
t
commit
|
commitdiff
|
tree
2013-10-10
Ber
k
Hess
fixed nbnxn 4x
8
p
air
s
earch without AVX
commit
|
commitdiff
|
tree
2013-10-02
Berk Hess
Fix
e
s rea
c
tion f
i
e
l
d free energy bug
commit
|
commitdiff
|
tree
2013-09-24
Berk
H
ess
optimized generic SIMD invsqrt
commit
|
commitdiff
|
tree
2013-09-21
Berk Hess
f
i
x
e
d
multi
p
le dista
n
ce restrai
n
t
s with OpenMP
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
made free energy PM
E
k
e
rnel 40%
faster
commit
|
commitdiff
|
tree
2013-09-16
Berk Hess
mdrun without OpenMP with thread-
M
PI
n
ow uses
a
ll cores
commit
|
commitdiff
|
tree
2013-09-13
Berk H
e
ss
correc
t
e
d
g
rompp const
r
ai
n
t/DOF w
a
rning with v
s
ites
commit
|
commitdiff
|
tree
2013-08-25
Berk Hess
introduc
e
d n
b
nxn d
a
ta
struc
t
ur
e
for b
o
undin
g
bo
x
es
commit
|
commitdiff
|
tree
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