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Made gmx dos work again.
2016-06-27
David van der Spoel
Made gmx dos
w
ork again
.
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
Fix
b
ug with
fbposre
s
+MPI
+
Op
e
nMP
commit
|
commitdiff
|
tree
2016-05-08
M
ark Abraham
F
i
x
c
onstants, units and conversio
n
fact
o
rs
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d van der S
p
oel
Removed s
r
ene
w
that wa
s
mak
i
n
g
array sma
l
ler incorrect
l
y
.
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixed
nbnx
n
_4xN
p
e
rform
a
nce regressi
o
n
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
F
ix bu
g
s
with intermol
i
nteractio
n
s a
n
d DD
commit
|
commitdiff
|
tree
2015-09-29
David van
der
Spoel
F
ixe
s
b
ug in the computation of C
o
efficient of Therma
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-02
Béla Voß
Avoid integer overflow in gmx_w
h
am by using gmx_i
n
t64_t
.
commit
|
commitdiff
|
tree
2015-05-12
J
ochen Hub
OpenMP
p
aral
l
elization of g_wh
a
m
commit
|
commitdiff
|
tree
2015-04-09
David van der Spo
e
l
Clarified
c
omments
for time-d
e
pend
e
nt el
e
ctric f
i
elds
.
commit
|
commitdiff
|
tree
2015-04-08
David van der S
p
oe
l
Fixed incorrect
o
u
tput of
g
b_algorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2014-10-28
David van d
e
r S
p
oel
Even m
o
re refres
h
ing quotes
.
commit
|
commitdiff
|
tree
2014-09-22
Mar
k
A
b
r
a
ham
More
quotes
commit
|
commitdiff
|
tree
2014-09-22
E
r
ik Lind
a
hl
More quotes
commit
|
commitdiff
|
tree
2014-09-19
Teemu Murtola
Add support for cu
m
ula
t
ive histograms
commit
|
commitdiff
|
tree
2014-09-17
Da
v
id v
a
n
d
e
r
Spoel
Merge
r
elease-5-
0
i
nto master
commit
|
commitdiff
|
tree
2014-08-30
David van der
Spo
e
l
Fixes issue wit
h
vsit
e
n and verl
e
t
buffers
.
commit
|
commitdiff
|
tree
2014-06-25
David van der Spoe
l
A
dded
c
heck for domain de
c
ompo
s
ition a
n
d shell
s
.
commit
|
commitdiff
|
tree
2014-06-22
David van
der Spoel
Implemented fatal error
f
or
nstc
a
l
c
energy!=1 wi
t
h shells
.
commit
|
commitdiff
|
tree
2014-06-13
Berk
H
e
ss
Made shells
work
w
it
h
the Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk H
e
ss
Ma
d
e gmxcheck -rmsd work again with forces
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Make sure genrestr uses the disre_up
2
parameter
commit
|
commitdiff
|
tree
2014-06-12
Erik Linda
h
l
Remove
d
und
o
cumen
t
ed -map and -mdata o
p
t
i
o
n
s from
g
_sham
.
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Always
write output from genion
commit
|
commitdiff
|
tree
2014-06-11
David van d
e
r Spoe
l
Fixes
bug where -
e
an
d
-dt flags did not
w
ork anymor
e
.
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Made repl_ex time step more
r
eadab
l
e
commit
|
commitdiff
|
tree
2014-06-07
Teemu M
u
rtola
Improve (Selection|FileN
a
me)OptionManager ha
n
dl
i
ng
commit
|
commitdiff
|
tree
2014-06-07
T
e
emu Mur
t
ola
Replac
e
all command line p
a
rsin
g
wi
t
h Optio
n
s
commit
|
commitdiff
|
tree
2014-06-07
Te
e
mu Murtola
Move r
e
s
i
duetype handling to i
t
s ow
n
fil
e
.
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtol
a
Remove support f
o
r
"
old" index file format
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Fix bug writing TNG ou
t
p
u
t from
d
ump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lu
n
dborg
Bug
f
ix in the TNG libra
r
y
t
o imp
r
ov
e
rea
d
ing
.
commit
|
commitdiff
|
tree
2014-05-24
M
a
r
k
Abrah
a
m
Mo
v
e too
l
s code to wh
e
re it
is used
commit
|
commitdiff
|
tree
2014-05-18
Teemu Murtola
M
o
ve 3dview
.
* to programs/view/
commit
|
commitdiff
|
tree
2014-05-16
Dav
i
d van
der
S
poel
Fixe
s
a complica
t
ed bug in g
_
anaeig
.
commit
|
commitdiff
|
tree
2014-03-17
Teemu
M
ur
t
ola
Update
manual
analysis
s
ection
commit
|
commitdiff
|
tree
2014-02-21
Ni
n
a Fischer
Added n
e
w a
m
b
e
r99sb-
i
ld
n
-bsc0 f
o
rc
e
fie
l
d
.
commit
|
commitdiff
|
tree
2014-02-10
David van der S
p
oel
Mo
v
ed con
d
iti
o
nal
cma
k
e code for
v
m
d
io
.
commit
|
commitdiff
|
tree
2014-01-19
Mark Abraham
C
l
ean up aft
e
r
gmxcpp
commit
|
commitdiff
|
tree
2013-12-23
David va
n
der S
p
oe
l
Fixed
c
ompilat
i
o
n
issue due to gcc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
D
a
vid van der
S
p
o
e
l
Fixe
s
#
1
3
1
2 uninitialized error
in g_enema
t
.
commit
|
commitdiff
|
tree
2013-05-16
Da
v
id va
n
der
Spoe
l
Fixed two
c
ompil
a
tio
n
i
s
sues
.
commit
|
commitdiff
|
tree
2013-05-02
David van der Spoel
Fi
x
es #
1
238 g_h
y
dorder does not call set_pbc
.
commit
|
commitdiff
|
tree
2013-03-07
Da
v
id van d
e
r
S
p
o
el
Fixes #118
3
PBC bu
g
in
g_mi
n
dist
commit
|
commitdiff
|
tree
2013-02-13
Dav
i
d van der Spo
e
l
P
lain t
e
xt quotes
.
commit
|
commitdiff
|
tree
2012-11-26
Davi
d
van
der Spoel
Fi
x
es #
1
035 NaN
in g
_
cluster outp
u
t
.
commit
|
commitdiff
|
tree
2012-11-20
David van der Spoel
Fixes bug in g_hbond th
a
t makes it
pro
d
uce fatal error
.
commit
|
commitdiff
|
tree
2012-10-21
David v
a
n der
Spoel
Fixed Bug #593 about me
m
ory
h
ole in trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
Davi
d
van der Spoel
Set r
e
turn value
t
o
FALSE (0)
in estima
t
e_
d
t in libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-07
David van d
e
r Spoel
A
d
apte
d
NMR
r
ela
t
ed data to new p
d
b for
m
a
t
.
commit
|
commitdiff
|
tree
2012-09-04
Da
v
i
d
van der Spoel
Made tut
o
rial slightl
y
les
s
c
onfusing
.
commit
|
commitdiff
|
tree
2012-08-16
David van
d
er Spoel
Optional compu
t
atio
n
o
f fluct
.
props
i
n
g
_energy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
David van der Spoe
l
F
ixed b
u
g in free energ
y
cal
c
ulation
f
o
r Morse potenti
a
ls
commit
|
commitdiff
|
tree
2012-06-21
David van der Spoel
Fi
x
es #961 - Shake rep
o
rts wrong
error
commit
|
commitdiff
|
tree
2012-03-17
Davi
d
va
n
der Spoel
Removed q
h
o
p files from this branch
.
commit
|
commitdiff
|
tree
2012-03-10
David van der
Spoe
l
Vibration s
p
e
ctra from velocity
ACF
o
r Normal modes
.
commit
|
commitdiff
|
tree
2012-01-31
D
avid van der Spo
e
l
Changed order of parameters in t
o
p file
commit
|
commitdiff
|
tree
2012-01-25
David van der
S
poel
Added tw
o
new bo
n
de
d
functio
n
s
.
commit
|
commitdiff
|
tree
2012-01-17
David van
der Spo
e
l
Repla
c
e stderr by st
d
out in editco
n
f termin
a
l outp
u
t
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
D
avid van der Spoel
In
t
roduced fat
a
l
e
r
ror i
n
grompp for incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David v
a
n der Sp
o
e
l
Commented out part of t
h
is new program that was
n
o
t
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David
van der
S
poe
l
F
i
x
e
d
documentation issue described in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Dav
i
d van der Spo
e
l
Fixed d
o
cume
n
tat
i
on i
s
su
e
d
escribed
in red
m
ine
issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David van de
r
Spoel
F
ixed comp
i
lation issue
s
commit
|
commitdiff
|
tree
2011-09-19
David van d
e
r Spoe
l
Resolved ge
r
rit is
s
ue
h
ttps:/
/
ger
r
it
.
g
r
omacs
.
org/#change
,
126
commit
|
commitdiff
|
tree
2011-09-13
David van der Spoel
Added warning line
.
commit
|
commitdiff
|
tree
2011-07-20
David
van der S
p
oel
Mer
g
e b
r
anch 'r
e
le
a
s
e
-
4-5-patch
e
s' of gi
t
@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
David van
d
er S
p
oel
Ad
d
ed initi
a
lization of array
s
a
f
t
e
r srenew c
a
ll
.
commit
|
commitdiff
|
tree
2011-07-20
David van der
S
poel
Added init
i
a
lization of arrays after sre
n
e
w cal
l
.
commit
|
commitdiff
|
tree
2011-07-02
David van
d
er Spoel
M
e
rge
branch 'mast
e
r
' of git@git
.
gromacs
.
org:
g
r
o
macs
commit
|
commitdiff
|
tree
2011-07-02
David van der Spoel
Compila
t
ion fi
x
e
s in gmx_den
s
ity
.
c and hi
s
t
o
gra
m
.
cpp
commit
|
commitdiff
|
tree
2011-07-01
Da
v
id van d
e
r Spoel
Merge
branc
h
'release-4-5
-
p
a
tches' of git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Da
v
id
van der Spoel
Merge b
r
anch
'rele
a
se-4
-
5-patche
s
' o
f
g
i
t
@
g
it
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
D
a
vid
van der Spoel
Add
e
d
g_dos target
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van der
S
poel
Further patches to fluctua
t
ion code and
d
e
n
s
i
ty
o
f
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
av
i
d van
d
er
Spoel
Added computation o
f
A and U
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Updated, made de
f
ault toleranc
e
f
or bisecto
r
m
o
re s
t
ringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David v
a
n de
r
Spoel
Fixed we
i
ght functi
o
ns
and added -dump option (hi
d
den
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van de
r
Sp
o
el
Updated
.
Fixed computat
i
on of fr
e
quency
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
Updated the eqn for com
p
uting Delta
.
Now get
r
ough
l
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van
d
er Spoel
Mult
i
plied t
h
e DoS
b
y the ti
m
e
s
tep (between f
r
ames)
.
commit
|
commitdiff
|
tree
2011-05-31
D
avid van der Spoel
Upda
t
e
d
.
Now c
o
m
p
utes diffusion from the VACF
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id va
n
der
S
poel
F
i
x
e
d
x-axi
s
t
o
b
e in re
c
iproc
a
l cm
.
commit
|
commitdiff
|
tree
2011-05-31
D
avid v
a
n de
r
S
poel
Furthe
r
upd
a
tes
.
Still n
o
t perfe
c
t
.
commit
|
commitdiff
|
tree
2011-05-31
D
avid van der Spoel
A
d
d
ed stuff to compute cP
a
nd S
.
N
o
t co
m
plete
y
et
.
commit
|
commitdiff
|
tree
2011-05-31
David van
de
r
Spoel
Updated to comput
e
the f
l
uid
i
city
.
Added ref
s
f
o
r
citatio
n
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Updated
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van der
S
poel
New
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id va
n
der Spoel
Further patches
t
o fluctuat
i
on code an
d
density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d van der Spoel
M
erg
e
b
r
anc
h
'master' of
git@git
.
g
r
omacs
.
org:
g
rom
a
cs
commit
|
commitdiff
|
tree
2011-05-31
David van der Spo
e
l
Added qu
o
te
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
Further pat
c
hes to fluctu
a
t
i
o
n code and de
n
si
t
y of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der Spoel
Added quote
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d van d
e
r S
p
o
e
l
Me
r
ge
b
ranch 'relea
s
e-4-5-
p
atche
s
'
o
f
git@git
.
gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van der Spoel
Mer
g
e
b
ra
n
ch
'
r
elease-4-5-p
a
tche
s
' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van de
r
Spo
e
l
Re-imp
l
emented the
f
luct
u
at
i
o
n
analysis, based on Enthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van
d
er Spoel
Re-
i
mplem
e
n
ted the
f
l
uct
u
at
i
o
n
an
a
l
y
sis, based on Enthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-07
D
avi
d
van der Spoel
Added computation of A and U
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
vid van
der Sp
o
el
Updated,
made default tolerance for b
i
secto
r
mor
e
stringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
v
id va
n
d
er Spoel
Fixed weight functions an
d
added -dump option
(hidden
.
.
.
commit
|
commitdiff
|
tree
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