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GROMACS 2021 first beta release
2020-10-09
Berk Hess
A
d
d MTS support for pull and AWH
commit
|
commitdiff
|
tree
2020-10-05
Ber
k
Hes
s
Re
m
o
v
e incorrect cy
c
le suppressio
n
commit
|
commitdiff
|
tree
2020-10-01
Berk Hess
Move compute
S
lowF
o
rces into
stepWork
commit
|
commitdiff
|
tree
2020-09-30
Berk Hess
Move com
p
uteSlowForces into stepWork
commit
|
commitdiff
|
tree
2020-09-28
Berk Hess
Fix di
s
persion
correction ta
b
l
e
generation
commit
|
commitdiff
|
tree
2020-09-25
B
e
rk Hess
Fix
g
r
o
mpp
group han
d
ling with fr
o
zen system
commit
|
commitdiff
|
tree
2020-09-18
B
e
r
k Hess
Re
m
o
v
e
cu
t
of
f
_
s
c
h
e
me from
t
_force
r
ec and inter
a
ction_
c
onst_t
commit
|
commitdiff
|
tree
2020-09-17
Berk
Hess
Move bNo
n
bonded fl
a
g from t_for
c
e
rec to
S
i
mulationWorkload
commit
|
commitdiff
|
tree
2020-09-16
Berk Hess
Remove unnec
e
ssary condi
t
ion
in
D
D for
c
e
b
uf
f
er resi
z
i
n
g
commit
|
commitdiff
|
tree
2020-09-15
Be
r
k Hess
Only
e
x
t
e
nd Ew
a
ld table when necessary
commit
|
commitdiff
|
tree
2020-09-15
Berk Hess
F
i
x task assignment with mu
l
tirun
s
commit
|
commitdiff
|
tree
2020-09-13
Berk
H
ess
Decouple nsttcoupl
e
and ns
t
pcouple from nstlist
commit
|
commitdiff
|
tree
2020-09-10
Berk Hess
Add a
n
gles to ListedF
o
rces selections
commit
|
commitdiff
|
tree
2020-09-10
Berk Hess
Fix
m
emory
c
orruption wi
t
h
strings in g
r
ompp
commit
|
commitdiff
|
tree
2020-09-02
Berk
H
e
s
s
Move lis
t
ed and
wa
l
l
f
orces out of do_for
c
e_lowlevel()
commit
|
commitdiff
|
tree
2020-09-02
Berk Hess
Enable s
p
litting of lis
t
ed interaction calculation
commit
|
commitdiff
|
tree
2020-08-28
Berk Hess
A
dd
S
IMD
version
o
f
harmoni
c
bond
s
commit
|
commitdiff
|
tree
2020-08-27
Be
r
k Hess
Add Fo
r
ceBuff
e
rs class
commit
|
commitdiff
|
tree
2020-08-14
Berk Hess
Add SIMD bonded
t
ests an
d
impr
o
ve SIM
D
angles()
commit
|
commitdiff
|
tree
2020-08-13
Ber
k
Hess
Add n
e
w FEP perturbation che
c
k
functions
commit
|
commitdiff
|
tree
2020-08-12
Berk H
e
ss
Fix virtual site vsiten
i
ndexing
b
ug
commit
|
commitdiff
|
tree
2020-08-07
Berk Hess
Add acc
u
mulat
i
on checks to Forei
g
nLambdaTerms
commit
|
commitdiff
|
tree
2020-07-31
B
erk He
s
s
Move forei
g
n potential energ
y
accu
m
ul
a
tion
commit
|
commitdiff
|
tree
2020-07-06
Berk Hess
Mov
e
foreign potenti
a
l e
n
ergy acc
u
mulation
commit
|
commitdiff
|
tree
2020-06-26
Berk
H
ess
Move dispersio
n
correction cal
l
t
o do_forc
e
()
commit
|
commitdiff
|
tree
2020-06-24
Berk Hess
A
d
d class Liste
d
Forces
commit
|
commitdiff
|
tree
2020-06-24
Be
r
k Hess
Chan
g
e grompp disres cost t
o
linear
commit
|
commitdiff
|
tree
2020-06-23
Berk Hess
Add virtual site with one con
s
truct
i
ng atom
commit
|
commitdiff
|
tree
2020-06-22
Berk H
e
ss
Fix tpxio funct
i
on
t
y
pe upd
a
te
t
able
commit
|
commitdiff
|
tree
2020-06-22
Berk Hess
Move
s
oft-core pa
r
am
e
ters to interacti
o
n_
c
ons
t
_t
commit
|
commitdiff
|
tree
2020-06-18
Berk
Hes
s
Con
v
ert
t
_
f
o
rcetab
l
e to C
+
+
commit
|
commitdiff
|
tree
2020-06-05
Berk Hess
Remove CO
M
fro
m
SETTLE
commit
|
commitdiff
|
tree
2020-06-03
Be
r
k Hess
Fix
m
issing PBC
i
n
SHAK
E
commit
|
commitdiff
|
tree
2020-06-03
B
erk Hess
Turn Se
t
tleData
into a cla
s
s
commit
|
commitdiff
|
tree
2020-05-20
Berk Hess
Remove t_mdatoms from
Nbnxm s
e
tAtomP
r
ope
r
ti
e
s()
commit
|
commitdiff
|
tree
2020-05-19
Berk
H
e
ss
Refactor print_missing_interact
i
ons()
commit
|
commitdiff
|
tree
2020-05-14
Berk
He
s
s
Extract postProcessF
o
r
ceWithShiftForces(
)
commit
|
commitdiff
|
tree
2020-05-12
Ber
k
H
ess
Extra
c
t hel
p
er force
b
uffers
t
o a separate class
commit
|
commitdiff
|
tree
2020-05-12
Berk Hess
Refact
o
r
virt
u
al site inter
f
ac
e
commit
|
commitdiff
|
tree
2020-05-07
Berk Hess
Av
o
i
d warning durin
g
PME tunin
g
commit
|
commitdiff
|
tree
2020-04-06
B
erk
Hess
Mo
v
e
f
orce buffer resizi
n
g to mdsetup
commit
|
commitdiff
|
tree
2020-03-20
Berk Hess
Ren
a
m
e
class
G
rid to B
i
as
G
r
id
in AWH module
commit
|
commitdiff
|
tree
2020-03-19
Berk Hess
Simp
l
ify finish_update()
commit
|
commitdiff
|
tree
2020-03-19
Berk Hess
Re
m
o
ve at_start f
r
om t_graph
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
R
e
move use of gr
a
ph in do_force(
)
commit
|
commitdiff
|
tree
2020-03-18
Berk He
s
s
U
se Wh
o
leMo
l
eculeT
r
ansform for orire
s
a
n
d epsilon-surface
commit
|
commitdiff
|
tree
2020-03-18
B
e
rk He
s
s
Add
W
holeMol
e
culeTransfor
m
cl
a
ss
commit
|
commitdiff
|
tree
2020-03-17
Berk Hes
s
Convert t_graph to C++
commit
|
commitdiff
|
tree
2020-03-17
Berk Hess
Disable Ewald di
p
ole
c
orrection wit
h
o
u
t
DD
commit
|
commitdiff
|
tree
2020-03-13
Berk
Hess
Add t
e
sts for Ewald su
r
fac
e
terms
commit
|
commitdiff
|
tree
2020-03-11
B
e
rk H
e
ss
Add tests for g
r
aph
commit
|
commitdiff
|
tree
2020-03-10
Berk He
s
s
Fix ty
p
e
in range a
n
d add
tes
t
s
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make shake work with
o
u
t
g
raph
commit
|
commitdiff
|
tree
2020-03-05
Berk Hes
s
A
d
d Interact
i
onDefinitio
n
s
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix ce
n
ter of
mass motion removal
with froze
n
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 with
p
a
r
tial C
O
MM removal
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix too
s
mall p
a
irlist buffer on Intel GPU
s
commit
|
commitdiff
|
tree
2020-02-21
B
e
rk Hess
Ad
d
f
a
t
al error when
multisim
r
uns sharing
s
tate have
.
.
.
commit
|
commitdiff
|
tree
2020-02-15
Berk H
e
ss
Re
m
ove 1
pulse
DD requ
e
st
commit
|
commitdiff
|
tree
2020-02-05
Berk
Hess
A
ct
u
ally fix
PME forces
with FE without p
e
rturbed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Berk Hess
Actu
a
lly fix PM
E
f
o
rces with
F
E without perturbed q/
L
J
commit
|
commitdiff
|
tree
2020-01-23
Ber
k
Hess
Fix DD
r
ank cou
n
t p
r
ime che
c
k
commit
|
commitdiff
|
tree
2020-01-22
B
e
r
k
H
ess
Mino
r
cleanup
i
n constrain
t
and she
l
lfc code
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Fix ill
e
gal memory access in PME
communication
commit
|
commitdiff
|
tree
2020-01-22
Berk
Hess
C
l
arify C
O
MM/pos
r
es grompp note
commit
|
commitdiff
|
tree
2020-01-20
B
e
rk Hess
Use ArrayRef(WithPaddi
n
g) in c
o
ns
t
raint code
commit
|
commitdiff
|
tree
2020-01-20
Berk H
e
ss
Use std::v
e
ctor in she
l
lfc
commit
|
commitdiff
|
tree
2020-01-17
Berk H
e
ss
Add check for shells and GPU
update
commit
|
commitdiff
|
tree
2020-01-16
Be
r
k Hess
Corre
c
t fixed redmine issu
e
id
from 3
2
97 to 329
6
commit
|
commitdiff
|
tree
2020-01-15
Berk Hess
F
ix multisim with parallel s
i
mulation
commit
|
commitdiff
|
tree
2020-01-13
Ber
k
H
ess
Avoid unnecessary exclusion generati
o
n
in D
D
commit
|
commitdiff
|
tree
2019-12-22
Berk Hess
Use
L
istOfLists for atom
to constraint
mapping
commit
|
commitdiff
|
tree
2019-12-22
Berk
Hess
Mov
e
nr
_
nonp
e
rturbed out of t_il
i
s
t
commit
|
commitdiff
|
tree
2019-12-19
Berk
Hess
Expand ListOfLi
s
ts
pushBack() functionali
t
y
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Rem
o
ve exclusions fr
o
m t_to
p
ology
commit
|
commitdiff
|
tree
2019-12-19
B
e
rk
H
ess
Fix
m
drun ap
p
e
n
ding invalidat
i
n
g
energy files
commit
|
commitdiff
|
tree
2019-12-18
Berk H
e
ss
Change grompp decoupling SD warnin
g
to note
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
A
dd note for COM re
m
o
v
al with posi
t
ion re
s
traints
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
U
se ListOfL
i
sts in
g
mx_mto
p
_
t
and gmx_localt
o
p_t
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
F
ix issues i
n
ListO
f
Lis
t
s
commit
|
commitdiff
|
tree
2019-12-12
Berk H
e
ss
A
d
d
class ListOf
L
ists
commit
|
commitdiff
|
tree
2019-12-02
Be
r
k
H
e
s
s
Add che
c
k for coup
l
ed cons
t
r
aint
s
for
C
U
D
A
u
p
d
ate
commit
|
commitdiff
|
tree
2019-12-02
Ber
k
H
e
ss
Extract L
I
NCS
C
UDA helper f
u
nctions
commit
|
commitdiff
|
tree
2019-11-29
Berk Hess
Merge "M
e
rge branch release-2019 into r
e
lease-20
2
0
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk
H
ess
Update documena
t
ion for NPT GPU upd
a
t
e
commit
|
commitdiff
|
tree
2019-11-28
B
e
rk He
s
s
Remove assertion fai
l
u
r
e in AWH
wit
h
out i
n
i
t
ial stage
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
Fix bug with GPU pressure sca
l
ing at non T-scal
i
ng
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Be
r
k Hess
Fix is
s
ues wi
t
h A
W
H wit
h
per
i
o
d
ic pu
l
ling
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Qu
i
et
pdb2
g
mx and
u
se gm
x
_
fatal
commit
|
commitdiff
|
tree
2019-11-19
B
e
rk H
e
ss
Fix bonde
d
atom co
m
municati
o
n
performance
commit
|
commitdiff
|
tree
2019-11-18
Berk Hes
s
Fix
i
ntermolecular
i
nt
e
ractions with DD
commit
|
commitdiff
|
tree
2019-11-14
B
e
rk Hess
Simplify t_f
o
rc
e
rec de
s
tru
c
t
ion
commit
|
commitdiff
|
tree
2019-11-07
Berk He
s
s
Fix
.
g
r
o large box writ
i
ng
commit
|
commitdiff
|
tree
2019-11-06
Ber
k
Hess
D
e
precated sc-r-power=48
commit
|
commitdiff
|
tree
2019-11-01
B
e
r
k
Hess
Add haveEwald
S
urfaceContribution to SimulationWorkload
commit
|
commitdiff
|
tree
2019-10-31
Be
r
k H
e
ss
Upda
t
e GPU up
d
ate restriction
s
commit
|
commitdiff
|
tree
2019-10-30
Berk Hess
Fix w
a
l
l
s
w
ith GPU updat
e
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Add mdrun GPU up
d
ate documen
t
a
tion
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Fix Ewald dipole correctio
n
w
ith GPU update
commit
|
commitdiff
|
tree
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