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Properly check if there are perturbed constraints or masses
2020-11-23
Magnu
s
L
u
ndborg
Pro
p
erly
check if
t
her
e
a
re pertu
r
bed constraints or
.
.
.
commit
|
commitdiff
|
tree
2020-11-05
Magn
u
s Lundborg
S
e
t p
b
c
atom_i
n
put in
o
rder t
o
p
as
s
l
a
ter checks
commit
|
commitdiff
|
tree
2020-11-03
Magnus
L
undborg
Rem
o
ve TODO r
e
garding AWH
cov
e
r thr
e
shold along lambda
.
.
.
commit
|
commitdiff
|
tree
2020-10-16
Magnu
s
Lundborg
When lo
a
d
i
ng AWH user
d
ata do
not convolve the
bia
s
.
.
.
commit
|
commitdiff
|
tree
2020-10-09
Magnus Lund
b
org
AWH: Remove random term
from FEP tests
commit
|
commitdiff
|
tree
2020-09-21
Magnus Lundborg
AWH avoid constructor
s
onl
y
d
i
ffering in parameter
.
.
.
commit
|
commitdiff
|
tree
2020-09-03
Magnus Lundborg
P
r
int lambda state
to log f
i
le i
f
using AWH fo
r
F
EP
.
commit
|
commitdiff
|
tree
2020-08-25
M
agn
u
s Lund
b
org
Avoid log(0) if probability i
s
too l
o
w
commit
|
commitdiff
|
tree
2020-08-20
Mag
n
u
s Lu
n
d
borg
M
ake it
possi
b
le to
u
se FE
P
la
m
bda states as a reaction
.
.
.
commit
|
commitdiff
|
tree
2020-07-20
Magnus Lundborg
Two s
e
ts of coeffici
e
nts fo
r
Coulomb FEP P
M
E o
n
GPU
commit
|
commitdiff
|
tree
2020-03-04
Magnu
s
Lundbor
g
Separate
AWH parameter reading and checking
commit
|
commitdiff
|
tree
2020-03-03
Mag
n
us Lundborg
Store dHdL f
o
r all neighbo
r
la
m
bdas
commit
|
commitdiff
|
tree
2020-02-25
M
a
gnus Lundborg
Fix out of sync
checkp
o
int files in simulations shar
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lundborg
More SIMD preparations in the FE calculations
commit
|
commitdiff
|
tree
2020-01-24
Magnus Lundborg
Removed SC RPower 48 fr
o
m FEP kernel
commit
|
commitdiff
|
tree
2020-01-23
Magnus Lundborg
Minor cosmetic im
p
rove
m
ent
s
in AWH
commit
|
commitdiff
|
tree
2019-09-24
Magnus Lundborg
Add
.
p
a
rt0001
.
to f
i
les from th
e
first run with -noappend
.
commit
|
commitdiff
|
tree
2019-09-11
Magnus Lundborg
Ti
d
y up the
FE kernel
commit
|
commitdiff
|
tree
2019-09-10
Magnu
s
Lun
d
borg
More templati
n
g
o
f gmx_nb_free_energy_kernel()
commit
|
commitdiff
|
tree
2019-09-04
Ma
g
nus Lun
d
b
org
Inline fu
n
ctio
n
s of
cal
c
ul
a
tio
n
s
o
f F
E
interac
t
ion
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Mag
n
u
s Lun
d
borg
C
hanged some variable
s
fro
m
SCReal to real in
F
E kernel
.
commit
|
commitdiff
|
tree
2019-07-03
Magnus Lund
b
org
Vectoriz
e
GPU bonded dat
a
.
commit
|
commitdiff
|
tree
2019-06-30
Magnus L
u
n
dborg
Clean
i
ng up
t
he G
P
U bonded kernel
commit
|
commitdiff
|
tree
2019-06-28
M
a
gnus Lund
b
org
Fuse
d
G
PU b
o
n
d
ed kernels
commit
|
commitdiff
|
tree
2018-12-14
M
a
gnus Lundborg
Se
t
HAVE_LMFIT properly
commit
|
commitdiff
|
tree
2018-11-29
Magnus
Lundbo
r
g
Make p
u
ll wi
t
h COM fr
o
m previ
o
u
s step work w
i
th MPI
commit
|
commitdiff
|
tree
2018-10-16
M
a
gnus L
u
ndbo
r
g
Move
g
mx_ffpa
r
ams_t
to forcefiel
d
p
a
rameters
commit
|
commitdiff
|
tree
2018-10-15
Magnu
s
L
u
ndborg
Enable output of a
v
erage pu
l
l f
o
rce and posi
t
ions
.
commit
|
commitdiff
|
tree
2018-10-03
Magnus Lundborg
All
o
w using COM of p
r
e
vious step
as PBC reference
commit
|
commitdiff
|
tree
2018-09-26
Magnus
Lundbor
g
Added p
u
llCheckPbcWi
t
hin
G
roup() to
c
h
e
ck on
e
g
r
oup
commit
|
commitdiff
|
tree
2018-09-25
M
a
g
n
us Lundborg
Ad
d
m
ar
g
in as input to
p
ullGroupObeysPbcRestrictions
commit
|
commitdiff
|
tree
2018-09-21
Magnus Lundb
o
rg
F
i
xes a bug in
pull group
s
ize c
a
lc
u
lation
commit
|
commitdiff
|
tree
2018-09-07
Magnu
s
Lund
b
o
r
g
C
h
eck q
p
ert
u
rbatio
n
w
h
en
PME on GPU is tested
commit
|
commitdiff
|
tree
2018-06-04
M
agnus Lundb
o
rg
Write la
m
bdas and bo
x
t
o
TNG at correct intervals
commit
|
commitdiff
|
tree
2018-03-29
Magnus
Lundbo
r
g
Improved check
of if only force
s
are comput
e
d
i
n d
o
_pair
s
()
commit
|
commitdiff
|
tree
2017-12-05
Magnus
L
undborg
S
I
MD accelera
t
ed Urey-Brad
l
ey
commit
|
commitdiff
|
tree
2017-11-18
Magnus Lundb
o
r
g
A
d
d
e
d Magnus Lundborg
a
s c
o
ntributor in the manual
.
Added
Magnus Lundborg
as contributor in the manual.
commit
|
commitdiff
|
tree
2017-11-08
Magnus L
u
ndborg
Update t
o
TNG
v 1
.
8
.
1
commit
|
commitdiff
|
tree
2017-10-13
Magnus L
u
ndbor
g
Do not include
h
eader
s
related t
o
O
b
se
r
v
ablesHist
o
ry
commit
|
commitdiff
|
tree
2017-10-03
Magnus
L
u
nd
b
org
W
r
ite atom masses and partia
l
charges to T
N
G
commit
|
commitdiff
|
tree
2017-06-11
Magnus
L
undborg
U
pdated
TNG to version 1
.
8
commit
|
commitdiff
|
tree
2015-12-05
Magnus Lundborg
Wr
i
te force
s
a
n
d velociti
e
s
to compres
s
e
d
TNG
.
commit
|
commitdiff
|
tree
2015-11-30
Magn
u
s Lundborg
Fixed typo
s
in
o
utp
u
t
.
commit
|
commitdiff
|
tree
2015-11-25
Ma
g
nus
Lu
n
dborg
Use lo
c
a
l
variables
i
nstead of those in
*
i
r
.
commit
|
commitdiff
|
tree
2015-06-24
Magnus Lundborg
Update
h
eader
when app
e
nding to TN
G
fi
l
e
.
commit
|
commitdiff
|
tree
2015-06-12
Magnus
Lundborg
TNG version 1
.
7
.
6
commit
|
commitdiff
|
tree
2015-05-16
Magnus
L
u
ndbo
r
g
T
N
G version 1
.
7
.
5
commit
|
commitdiff
|
tree
2015-04-21
Magnus
L
undb
o
rg
TNG versi
o
n 1
.
7
.
3
commit
|
commitdiff
|
tree
2014-11-24
Magn
u
s Lundborg
Wh
e
n
w
r
itin
g
T
N
G
the inpu
t
must
c
ontain m
o
lecu
l
e data
.
commit
|
commitdiff
|
tree
2014-09-02
Magnu
s
Lun
d
borg
TNG
Fix for GMX_DOU
B
LE builds an
d
w
h
ere ZLIB is
n
ot
.
.
.
commit
|
commitdiff
|
tree
2014-09-02
Magnus Lundborg
Fix
data block
l
ength when
u
ncompressing TNG data
.
commit
|
commitdiff
|
tree
2014-09-01
M
a
g
n
us L
u
ndborg
T
N
G
: Handle large file
s
on
3
2 bit
s
ystems
.
commit
|
commitdiff
|
tree
2014-09-01
Magnus Lundb
o
rg
Whe
n
writing TNG incl
u
de file closi
n
g in w
a
llcy
c
l
e
.
commit
|
commitdiff
|
tree
2014-08-21
Ma
g
nus Lundborg
Fix
e
d TNG memory
alignment
problem an
d
reset
p
ointers
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lu
n
dborg
Fi
x
bu
g
causin
g
rea
d
ing
next
frame not
to stop
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus
L
undborg
F
i
x tng_
n
um_frame_sets_g
e
t() with no fr
a
m
e
sets
.
commit
|
commitdiff
|
tree
2014-06-28
M
a
gnus Lundborg
Upd
a
te TNG b
u
i
l
d system
commit
|
commitdiff
|
tree
2014-06-24
Magn
u
s Lun
d
bo
r
g
Imp
r
oved ch
e
ck to decide if to
a
dd cha
i
n/residu
e
.
commit
|
commitdiff
|
tree
2014-06-19
M
a
gnus
L
u
n
dborg
B
u
mped the TNG library to the late
s
t ver
s
i
o
n
.
commit
|
commitdiff
|
tree
2014-05-31
Ma
g
nus L
u
ndb
o
rg
Fix
b
ug w
r
iti
n
g TNG output
f
r
o
m dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lu
n
dborg
Bug fix in the T
N
G
library to
i
m
prove reading
.
commit
|
commitdiff
|
tree
2014-04-24
Ma
g
nus Lu
n
dborg
More ef
f
ic
i
ent TN
G
s
e
lection gr
o
up cr
e
a
t
ion
commit
|
commitdiff
|
tree
2014-04-16
Magnus
L
undborg
Fixe
d
bug
i
nverting c
o
mpression precision
.
commit
|
commitdiff
|
tree
2014-03-01
Magnus Lundborg
Bum
p
ed TNG t
o
l
atest version
.
commit
|
commitdiff
|
tree
2014-02-13
Magnu
s
Lundb
o
r
g
One more b
u
mp of the TNG v
e
rsion
.
commit
|
commitdiff
|
tree
2014-02-13
Magnus
Lundbor
g
Removed
o
pti
o
n to
u
se OpenMP
w
i
t
h th
e
TNG lib
r
ary
.
commit
|
commitdiff
|
tree
2014-02-12
Magnus Lun
d
bo
r
g
Enable T
N
G builds on Windows
by
def
a
u
lt
.
commit
|
commitdiff
|
tree
2014-02-12
M
a
gnus Lundborg
B
umped
TNG to latest version
.
commit
|
commitdiff
|
tree
2014-02-11
Ma
g
nu
s
Lundborg
Added i
n
formation about
h
ow to cite the TNG
paper
.
commit
|
commitdiff
|
tree
2014-01-20
Magnus Lundborg
A
d
d TNG w
r
iting
and r
e
adin
g
suppor
t
commit
|
commitdiff
|
tree
2013-10-29
Ma
g
n
u
s Lundbo
r
g
F
i
xed memory
l
e
ak in gm
x
dump
.
commit
|
commitdiff
|
tree
2013-09-02
Magnus Lundborg
Set uppe
r
case
o
f FFTW
v
ariable at the rig
h
t
p
lace
.
commit
|
commitdiff
|
tree
2013-04-29
Magnus Lundborg
Fixe
s
"Func
t
ion type
U
-B no
t
i
m
plem
e
nted i
n
ip_per
t
.
"
commit
|
commitdiff
|
tree