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Correct user guide postion restraint virial
2019-05-14
Berk He
s
s
Correct us
e
r guide postion restraint vi
r
ial
commit
|
commitdiff
|
tree
2019-05-03
B
e
r
k Hess
Removed n
o
n
-
e
x
iste
n
t
AW
H
m
d
p
op
t
ion
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Mak
e
mdrun -nsteps w
o
r
k again
.
commit
|
commitdiff
|
tree
2019-04-15
Berk H
e
ss
Upda
t
e
2019 release notes for
i
ssue 2845
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
F
ix pdb-rel
a
ted issues
commit
|
commitdiff
|
tree
2019-04-15
B
e
rk
H
es
s
Disallow pull geometry direction-p
e
r
iod
i
c
with
A
WH
commit
|
commitdiff
|
tree
2019-03-11
Berk Hess
Add
grompp
w
arning with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-02-26
Berk Hess
Correc
t
g
ro
m
pp index file error
message
commit
|
commitdiff
|
tree
2019-02-15
Berk
H
ess
F
ix mass Delta H double countin
g
commit
|
commitdiff
|
tree
2019-02-09
Berk Hes
s
Disall
o
w rerun with per
t
urbed
m
asses o
r
constraint
s
commit
|
commitdiff
|
tree
2019-02-06
Berk Hess
Fix s
e
gfault
with
EM, DD and group sc
h
e
m
e
commit
|
commitdiff
|
tree
2019-02-01
Berk Hess
Fix
i
nc
o
rre
c
t
LJ repulsion f
o
r
c
e
switching on GPUs
commit
|
commitdiff
|
tree
2019-01-23
Berk Hes
s
Fix error w
i
t
h
2
D
/3D DLB
commit
|
commitdiff
|
tree
2019-01-09
Be
r
k Hess
Fix gcc
-
8 release warnings in tng_io
commit
|
commitdiff
|
tree
2019-01-03
Berk
H
ess
Fix segmen
t
ation fault in DD cod
e
commit
|
commitdiff
|
tree
2018-12-14
B
e
rk
Hess
Fix LINCS triangle constraining with OpenMP
commit
|
commitdiff
|
tree
2018-12-14
B
er
k
Hess
F
ixe
d
n
u
llptr derefence in LI
N
C
S
error
commit
|
commitdiff
|
tree
2018-12-14
Be
r
k Hess
Fix LINCS triangle constrai
n
ing with O
p
enMP
commit
|
commitdiff
|
tree
2018-12-12
Berk Hess
Temporary fix
for Ope
n
CL P
M
E gather
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Fix u
p
date groups with 2D/3D
D
LB
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Make large PME
grids work on GPU
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Docume
n
t mdrun mdp optio
n
modi
f
ication
commit
|
commitdiff
|
tree
2018-12-05
Berk Hess
Ad
d
updat
e
groups to
p
arallelization
d
oc
s
commit
|
commitdiff
|
tree
2018-12-05
Be
r
k Hes
s
M
a
ke
l
arge PM
E
grids wo
r
k on GPU
commit
|
commitdiff
|
tree
2018-11-26
Berk
H
ess
F
ix FP exception
i
n
p
ull code
commit
|
commitdiff
|
tree
2018-11-16
Ber
k
Hess
grompp now checks
t
au-p>=2*tau-t with NH+PR
commit
|
commitdiff
|
tree
2018-11-08
Berk
Hess
F
i
x bug with
D
D for
d
ims withou
t
PBC
commit
|
commitdiff
|
tree
2018-11-01
Berk Hess
Fix brok
e
n
u
p
date gro
u
ps
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Lim
i
t
a
u
to assignment of b
o
ndeds t
o
GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk H
e
ss
Pin im
p
ortant buffers in CUDA bondeds
commit
|
commitdiff
|
tree
2018-10-31
B
erk Hess
Work
a
roun
d
e
x
panded
e
n
s
embl
e
issues
commit
|
commitdiff
|
tree
2018-10-31
B
e
rk Hess
F
i
x
FP
exception in energ
y
reduction
commit
|
commitdiff
|
tree
2018-10-31
B
e
rk
H
ess
Co
r
rect V
V
integrator nstc
a
lcenergy use
commit
|
commitdiff
|
tree
2018-10-31
Be
r
k Hess
Correct grompp nste
x
pande
d
/nstc
a
lc
e
nergy check
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Add missi
n
g mass term to
delt
a
H
commit
|
commitdiff
|
tree
2018-10-23
Berk Hess
Add missing const
r
aint term to deltaH
commit
|
commitdiff
|
tree
2018-10-21
Berk Hess
Fix mdrun
s
tart
/
end ti
m
e print
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add
e
nv
.
v
ar
.
to disable upd
a
te grou
p
s
commit
|
commitdiff
|
tree
2018-10-12
B
e
rk
H
ess
Imp
l
ement assignin
g
bo
n
deds to t
h
e GPU
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Move
p
u
ll
o
utput functions to output
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
B
erk Hess
Minor refa
c
t
oring in
b
onded threading
commit
|
commitdiff
|
tree
2018-10-09
B
e
rk Hess
F
i
x
c
omp
i
ler warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enab
l
e update
groups
commit
|
commitdiff
|
tree
2018-10-05
Berk Hess
A
d
d
update groups to DD a
t
om displaceme
n
t
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Make AVX2 pass TSA
N
commit
|
commitdiff
|
tree
2018-10-04
Berk
H
ess
Add note
to avoid constraints=all-bonds
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
R
emove
u
n
n
e
c
es
s
ary
clearing in
gmxcpp
commit
|
commitdiff
|
tree
2018-10-03
Berk
H
e
ss
Convert gm
x
_cpp to C++
commit
|
commitdiff
|
tree
2018-10-02
Berk H
e
ss
U
p
d
ate DD
c
ut
o
ffs for update groups
commit
|
commitdiff
|
tree
2018-09-30
B
e
rk Hess
C
o
r
rect u
p
date group angle para
m
type
commit
|
commitdiff
|
tree
2018-09-29
Berk
Hess
Re
f
actoring in calc_v
e
rletbuf
.
c
p
p
commit
|
commitdiff
|
tree
2018-09-29
B
e
rk Hess
Add
U
p
dateGroups
C
og to DD
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
Move maxRef
e
renc
e
Temperature() to inp
u
trec
commit
|
commitdiff
|
tree
2018-09-27
Ber
k
Hess
Improve upd
a
te group ra
d
ii
commit
|
commitdiff
|
tree
2018-09-27
Berk Hess
R
eorga
n
ize RVe
c
scaling
functions
commit
|
commitdiff
|
tree
2018-09-26
Berk H
e
ss
Extract sett
l
e test water
c
o
o
rdinates
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Support atom groups
i
n
nbnxn_search
commit
|
commitdiff
|
tree
2018-09-25
Berk
H
ess
A
dd U
p
d
ateGr
o
upsCog class
commit
|
commitdiff
|
tree
2018-09-24
Berk H
e
s
s
Fix p
e
rfo
r
mance repo
r
t w
h
en in
i
t_
s
tep!=0
commit
|
commitdiff
|
tree
2018-09-22
Ber
k
Hess
Add update gro
u
ps boolean
t
o DD
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Rena
m
e DD c
o
ns
t
raint booleans
commit
|
commitdiff
|
tree
2018-09-22
B
erk Hess
Add update groups
commit
|
commitdiff
|
tree
2018-09-20
Berk
H
es
s
Change pull buff
e
rs to std::vecto
r
commit
|
commitdiff
|
tree
2018-09-20
Berk He
s
s
Fix type bug in tril
i
nic DD
code
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Convert gmx_cma
p
_t to C++
commit
|
commitdiff
|
tree
2018-09-19
Berk Hess
Conve
r
t
gm
x
_ffparams_t to C++
commit
|
commitdiff
|
tree
2018-09-18
B
e
rk Hes
s
Int
r
odu
c
e extractILists helper function
commit
|
commitdiff
|
tree
2018-09-18
Berk Hes
s
Refactor d
d
box
handl
i
ng
commit
|
commitdiff
|
tree
2018-09-17
Berk H
e
ss
Move ifunc
s
tuf
f
f
rom
idef
.
h to ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Ber
k
Hess
C
hange pointers to
I
nteractionList
t
o refer
e
n
c
e
s
commit
|
commitdiff
|
tree
2018-09-16
Berk Hess
R
e
factoring in
DD redis
t
ribute
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
R
e
factor getAtomGroupDis
t
ributio
n
()
commit
|
commitdiff
|
tree
2018-09-14
Berk Hess
Change gmx_moltype_t
.
i
l
i
s
t
to In
t
eraction
L
ists
commit
|
commitdiff
|
tree
2018-09-13
Berk
H
ess
Ad
d
C++ version o
f
t_ilist
commit
|
commitdiff
|
tree
2018-09-12
B
e
rk Hess
Con
v
ert
vsite s
t
ructs to C
+
+
commit
|
commitdiff
|
tree
2018-09-12
B
erk He
s
s
Convert DD gmx_
r
e
ver
s
e
_top_t to C++
commit
|
commitdiff
|
tree
2018-09-10
Be
r
k Hess
Fix PME for
c
e
s with F
E
without perturbed q/L
J
commit
|
commitdiff
|
tree
2018-08-29
Berk Hess
Refa
c
tor wall
po
t
ential c
a
lcu
l
a
tion
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Replace g
m
x_hash
_
t
by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Merge "Merg
e
branch r
e
lea
s
e-2018"
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk Hess
Add size
optimi
z
at
i
o
n
to Hash
e
dMa
p
commit
|
commitdiff
|
tree
2018-08-24
Berk Hess
Add t
e
sts for
Ha
s
hedMap
commit
|
commitdiff
|
tree
2018-08-22
Berk
H
ess
Fix
missin
g
interacti
o
ns with GPU and DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hes
s
Ensure domains are large enough
f
or at
o
m
moti
o
n
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
Fixed mdrun segv
with QM/M
M
ONIOM
scheme
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Refacto
r
calc_v
e
rlet
_
buffer_siz
e
()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Remove
c
o
m
pa
c
ting from
DD redis
t
ribute
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verl
e
t buff
e
r
estima
t
e
with
B
D
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix clan
g
names
p
ace comment
war
n
in
g
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fi
x
asser
t
ion failure in CG
commit
|
commitdiff
|
tree
2018-08-20
Berk Hes
s
Reall
y
fix CG with multiple domains
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
M
a
ke g
m
x
_ga2la_t a pr
o
per class
commit
|
commitdiff
|
tree
2018-08-18
Berk He
s
s
Add che
c
k for pull group PBC to grompp
commit
|
commitdiff
|
tree
2018-08-17
B
e
rk Hess
Make pull pb
c
atom use Loc
a
lAtomSe
t
commit
|
commitdiff
|
tree
2018-07-18
Berk Hess
Apply
l
ocal atom set
s
in pull
code
commit
|
commitdiff
|
tree
2018-07-03
Berk Hess
C
onvert
gmx_hash_t to C++
commit
|
commitdiff
|
tree
2018-07-03
Berk
Hess
L
o
ca
l
i
z
e
v
a
riables in dd_re
d
istribut
e
_cg()
commit
|
commitdiff
|
tree
2018-07-02
Berk
Hess
C
onvert DD
DLB cell
si
z
e handling to C
+
+
commit
|
commitdiff
|
tree
2018-07-02
Ber
k
Hess
Fix recent bug wi
t
h 2D/3D
D
LB
commit
|
commitdiff
|
tree
2018-07-01
Berk Hess
Removed smalloc
.
h from
m
any DD files
commit
|
commitdiff
|
tree
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