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Third GROMACS 2021 beta release
2020-11-11
Berk Hes
s
Update gmx
msd documentation
commit
|
commitdiff
|
tree
2020-11-10
Berk Hess
Fix dHdl and foreign energy clearing
a
t
checkpointing
commit
|
commitdiff
|
tree
2020-11-09
B
erk Hess
Move
i
mp
l
ementation
t
o cpp
file
commit
|
commitdiff
|
tree
2020-11-05
Berk
H
e
s
s
Disabl
e
MTS with
SD integrator
commit
|
commitdiff
|
tree
2020-11-05
Berk
H
es
s
Copy posit
i
on
r
es
t
ra
i
nt parameters with MT
S
commit
|
commitdiff
|
tree
2020-10-28
Berk
H
ess
Correct AWH initial histo
g
ram size
commit
|
commitdiff
|
tree
2020-10-21
Berk Hess
F
ix pull
c
o
de bug wit
h
DD an
d
atom sets
commit
|
commitdiff
|
tree
2020-10-09
Berk Hess
A
d
d
MTS
support for pull and
A
W
H
commit
|
commitdiff
|
tree
2020-10-05
Berk
H
ess
R
emove i
n
correct c
y
cle
s
up
p
ression
commit
|
commitdiff
|
tree
2020-10-01
Berk Hess
Move
c
o
m
p
u
teSlowForce
s
into stepWork
commit
|
commitdiff
|
tree
2020-09-30
Berk Hess
M
ove comput
e
SlowForces
i
nto
stepWork
commit
|
commitdiff
|
tree
2020-09-28
Be
r
k Hess
Fix
d
ispersion correction
t
a
ble gener
a
tion
commit
|
commitdiff
|
tree
2020-09-25
Berk
Hess
F
ix
g
rompp
group hand
l
ing wi
t
h froze
n
system
commit
|
commitdiff
|
tree
2020-09-18
B
er
k
H
ess
Remove cutoff_scheme
from t_forcere
c
a
nd interaction_const_t
commit
|
commitdiff
|
tree
2020-09-17
Berk Hess
Mov
e
bN
o
nbonded flag
f
rom t_forcerec
t
o
Si
m
u
lationWorkl
o
ad
commit
|
commitdiff
|
tree
2020-09-16
Berk Hess
R
e
mov
e
u
n
necessary c
o
ndition in DD forc
e
buffer re
s
i
z
i
n
g
commit
|
commitdiff
|
tree
2020-09-15
Berk Hess
Only ex
t
end Ewald
tabl
e
when necessary
commit
|
commitdiff
|
tree
2020-09-15
Berk
H
ess
Fix t
a
sk
assignment with
multiruns
commit
|
commitdiff
|
tree
2020-09-13
Berk Hess
D
e
coupl
e
n
s
ttcouple and nstpcouple
f
rom n
s
tlist
commit
|
commitdiff
|
tree
2020-09-10
Berk H
e
s
s
Add angl
e
s to List
e
dForces selections
commit
|
commitdiff
|
tree
2020-09-10
Berk Hess
Fi
x
memory corru
p
t
ion with str
i
ngs
i
n
g
rompp
commit
|
commitdiff
|
tree
2020-09-02
Berk Hess
Mov
e
listed and wall forces out
o
f do_force_l
o
wl
e
ve
l
()
commit
|
commitdiff
|
tree
2020-09-02
Berk Hess
Ena
b
le
s
pli
t
ting of liste
d
inter
a
ction calculat
i
on
commit
|
commitdiff
|
tree
2020-08-28
B
erk He
s
s
Add SIMD version o
f
h
a
rmonic
b
onds
commit
|
commitdiff
|
tree
2020-08-27
Berk Hess
Add
F
o
rceBuf
f
e
r
s
cl
a
ss
commit
|
commitdiff
|
tree
2020-08-14
Berk
Hess
Add
S
IMD bonded tests
and impr
o
v
e
SIMD angle
s
()
commit
|
commitdiff
|
tree
2020-08-13
Berk
H
ess
Add new FEP perturbati
o
n c
h
eck
f
un
c
t
ions
commit
|
commitdiff
|
tree
2020-08-12
Berk Hess
Fix v
i
rtual site vsiten indexing bug
commit
|
commitdiff
|
tree
2020-08-07
Berk
H
ess
Add
a
c
cumulation
c
hecks t
o
ForeignL
a
mbdaTerms
commit
|
commitdiff
|
tree
2020-07-31
B
e
r
k
H
e
ss
M
o
v
e forei
g
n
p
o
t
ential en
e
r
g
y acc
u
mulation
commit
|
commitdiff
|
tree
2020-07-06
Berk Hess
M
ove
f
ore
i
gn potential e
n
erg
y
accumulation
commit
|
commitdiff
|
tree
2020-06-26
Berk Hess
Mov
e
disp
e
rsion correction c
a
l
l
to do_for
c
e
(
)
commit
|
commitdiff
|
tree
2020-06-24
Berk Hess
Add class ListedForces
commit
|
commitdiff
|
tree
2020-06-24
Ber
k
Hess
Change gr
o
m
pp disre
s
cost to linear
commit
|
commitdiff
|
tree
2020-06-23
B
e
rk Hess
Add v
i
rtua
l
site
w
ith one constr
u
c
ting atom
commit
|
commitdiff
|
tree
2020-06-22
Be
r
k Hess
Fix tpxi
o
f
un
c
tion
type u
p
date table
commit
|
commitdiff
|
tree
2020-06-22
Berk
H
ess
M
o
ve soft-core par
a
me
t
ers to in
t
eraction_const_t
commit
|
commitdiff
|
tree
2020-06-18
B
e
rk Hess
Conve
r
t t_forcetable to C++
commit
|
commitdiff
|
tree
2020-06-05
B
erk He
s
s
Rem
o
ve CO
M
from SETTLE
commit
|
commitdiff
|
tree
2020-06-03
B
erk He
s
s
F
ix missing PBC in SHAKE
commit
|
commitdiff
|
tree
2020-06-03
B
e
rk Hess
Turn SettleD
a
ta into a
c
lass
commit
|
commitdiff
|
tree
2020-05-20
Berk Hess
R
emove t_
m
dato
m
s from
Nbnxm setA
t
omPr
o
pe
r
ties()
commit
|
commitdiff
|
tree
2020-05-19
Berk Hess
Ref
a
ctor print_missing_int
e
ractions()
commit
|
commitdiff
|
tree
2020-05-14
B
e
rk Hess
E
x
t
ract postProcessForceWit
h
ShiftFo
r
ces(
)
commit
|
commitdiff
|
tree
2020-05-12
Berk Hess
E
xtract helper
f
orce buffer
s
t
o
a sep
a
rate class
commit
|
commitdiff
|
tree
2020-05-12
B
erk H
e
s
s
Refactor virtual site interface
commit
|
commitdiff
|
tree
2020-05-07
B
erk Hess
Av
o
id warning during PME t
u
nin
g
commit
|
commitdiff
|
tree
2020-04-06
Berk Hess
Mov
e
force buffer resiz
i
ng to
m
dse
t
up
commit
|
commitdiff
|
tree
2020-03-20
Berk
H
ess
Re
n
ame
c
lass Grid to BiasGrid
in AW
H
module
commit
|
commitdiff
|
tree
2020-03-19
Berk Hess
Simplify fini
s
h
_u
p
date()
commit
|
commitdiff
|
tree
2020-03-19
Berk Hess
Re
m
ove at_start from
t
_graph
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
R
emove u
s
e
o
f
g
raph in do_for
c
e()
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
U
s
e WholeMoleculeTransform for orires
a
nd epsilon-sur
f
ace
commit
|
commitdiff
|
tree
2020-03-18
Be
r
k Hess
Add WholeMol
e
cule
T
r
ansform class
commit
|
commitdiff
|
tree
2020-03-17
Berk
H
ess
Convert t
_
g
r
aph to C++
commit
|
commitdiff
|
tree
2020-03-17
B
erk
Hess
Dis
a
b
l
e
E
wald dipole correction without DD
commit
|
commitdiff
|
tree
2020-03-13
Berk Hess
Add tests for Ewald surface te
r
ms
commit
|
commitdiff
|
tree
2020-03-11
Berk Hess
Add test
s
for g
r
a
p
h
commit
|
commitdiff
|
tree
2020-03-10
B
e
r
k
Hess
Fix type
in range and add tests
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Mak
e
shake
work wit
h
out graph
commit
|
commitdiff
|
tree
2020-03-05
B
erk He
s
s
Add
I
nterac
t
ion
D
efinitions
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix center of
m
ass
motio
n
remov
a
l
w
ith frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix
g
rompp unbound atom check
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix nrdf
w
it
h
parti
a
l COMM re
m
o
v
a
l
commit
|
commitdiff
|
tree
2020-03-02
Be
r
k Hess
Fix too
s
ma
l
l pairlist b
u
ffer
o
n
Intel GP
U
s
commit
|
commitdiff
|
tree
2020-02-21
Be
r
k Hess
A
dd fatal error
w
h
en
multisim
r
uns s
h
aring state have
.
.
.
commit
|
commitdiff
|
tree
2020-02-15
B
erk Hess
R
emo
v
e 1
p
u
lse D
D
request
commit
|
commitdiff
|
tree
2020-02-05
Berk
Hess
Actuall
y
fix PME forc
e
s with FE wit
h
out
pertu
r
bed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Berk Hess
Actually fix PME f
o
rce
s
with
FE wi
t
hout pertu
r
bed q/LJ
commit
|
commitdiff
|
tree
2020-01-23
Berk Hes
s
Fix DD rank c
o
unt pri
m
e
che
c
k
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Mi
n
or cleanup
i
n
c
o
nst
r
aint and shellf
c
code
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Fix illeg
a
l memory access in PM
E
communic
a
t
ion
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Cl
a
rify C
O
MM/posr
e
s g
r
omp
p
note
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use ArrayRef
(
W
ithPadd
i
ng) in constraint code
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use st
d
:
:vector in shellfc
commit
|
commitdiff
|
tree
2020-01-17
B
erk Hess
A
dd
c
heck for shells and GPU upd
a
t
e
commit
|
commitdiff
|
tree
2020-01-16
Berk
H
ess
Cor
r
ect fixed
redmine issue id from 3297 t
o
3296
commit
|
commitdiff
|
tree
2020-01-15
Berk Hess
F
ix multi
s
im with parallel
s
imu
l
atio
n
commit
|
commitdiff
|
tree
2020-01-13
Berk Hess
Avoid un
n
ecessary
e
xclusion gen
e
rat
i
on in DD
commit
|
commitdiff
|
tree
2019-12-22
B
e
r
k
He
s
s
U
s
e ListOfL
i
s
ts
for atom to const
r
a
i
nt ma
p
ping
commit
|
commitdiff
|
tree
2019-12-22
Berk
Hess
Mo
v
e nr_nonperturbed ou
t
of t
_
ilist
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Expand ListOfLists pushBack
(
) functional
i
ty
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
R
e
m
ove exclusion
s
f
rom t_topolo
g
y
commit
|
commitdiff
|
tree
2019-12-19
Be
r
k Hess
F
ix
m
d
run append
i
n
g
inv
a
lidating energy files
commit
|
commitdiff
|
tree
2019-12-18
B
erk Hess
Change grompp decoupling S
D
wa
r
ning to
n
ote
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
Add note for COM removal with
p
o
sition restraints
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Use ListOfLists in gm
x
_mtop_t and gm
x
_loc
a
l
t
op_t
commit
|
commitdiff
|
tree
2019-12-16
B
erk Hess
Fix issues in Lis
t
OfLis
t
s
commit
|
commitdiff
|
tree
2019-12-12
Berk Hess
Add
class ListOfLists
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
A
dd check for coupl
e
d constraints fo
r
CUDA update
commit
|
commitdiff
|
tree
2019-12-02
B
e
rk
H
e
ss
E
x
tract LINCS CUDA helper functi
o
ns
commit
|
commitdiff
|
tree
2019-11-29
Be
r
k Hess
Mer
g
e "Merge branch release-2019 into
r
elea
s
e-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
U
pdate
documenati
o
n for NPT
GPU update
commit
|
commitdiff
|
tree
2019-11-28
Berk H
e
ss
Remove assertion failure
in AWH without
initial stage
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
F
i
x
b
u
g with G
P
U
pr
e
ssure scaling at
non T-scaling
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
B
e
rk Hess
Fix
i
ssues with AWH
w
ith
p
eriod
i
c
pulling
commit
|
commitdiff
|
tree
2019-11-20
B
erk Hes
s
Quiet
p
db2gm
x
and use
g
mx_fa
t
al
commit
|
commitdiff
|
tree
2019-11-19
Berk
H
e
ss
F
ix
bonded
atom
c
ommu
n
ication performance
commit
|
commitdiff
|
tree
2019-11-18
B
er
k
Hes
s
Fix intermo
l
ecul
a
r interac
t
i
ons with
DD
commit
|
commitdiff
|
tree
2019-11-14
Berk
H
ess
Simplify t_f
o
r
c
erec destructio
n
commit
|
commitdiff
|
tree
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