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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2011-04-10
David van
d
e
r
S
poel
Merge branch 're
l
ease-4-5-patches'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
D
a
vid
van der Spoel
Add
e
d g_hydorder
.
1
man page
.
commit
|
commitdiff
|
tree
2011-04-06
David v
a
n de
r
Spoel
F
i
x
ed heade
r
for gmx_
c
onect_init
commit
|
commitdiff
|
tree
2011-04-04
David
v
an
d
er Spoel
New entry
commit
|
commitdiff
|
tree
2011-01-22
Davi
d
van d
e
r Spoel
Fixed bug 678 which
was due to calling g
m
x
_
fatal
w
i
thout
.
.
.
commit
|
commitdiff
|
tree
2010-12-23
David v
a
n der
S
poel
F
i
xed
b
ug in statistics which did no
t
a
llow fi
t
ting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Dav
i
d van der Spoel
Merg
e
branc
h
'release
-
4-5-patch
e
s' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Da
v
id van d
e
r Spoel
Added 1 quote
.
commit
|
commitdiff
|
tree
2010-11-28
D
a
v
i
d van
d
e
r
S
poel
Fi
x
ed bugz
i
ll
a
616 about form
a
tting in th
e
help text
.
commit
|
commitdiff
|
tree
2010-11-18
Da
v
i
d
van de
r
Spoel
Mad
e
printing
in check_mu
l
ti_init conditional, dependi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
David van de
r
S
poel
M
erge b
r
anch
'
r
elease-4-5-patches' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David van der Sp
o
el
Me
r
ge
b
ranch 'r
e
lease-4-5-patch
e
s
'
of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David
v
a
n
der
S
poel
Re-added g_k
i
n
etics to s
r
c/tools/Ma
k
efile
.
am
commit
|
commitdiff
|
tree
2010-09-24
David van der Spoel
U
p
d
ated to reflect bug 557
.
commit
|
commitdiff
|
tree
2010-09-16
D
a
vid van der Sp
o
el
Cor
r
ected name of one
o
f the
developers listed i
n
header
.
commit
|
commitdiff
|
tree
2010-09-14
David van
der
S
po
e
l
Fixed
bug 5
5
3
by checking whether an at
o
m nam
e
i
s
long
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
Davi
d
v
a
n d
e
r S
p
oel
F
ixed demo to work with new pdb2gmx that r
e
quires
t
w
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David va
n
der Sp
o
el
Made genrestr -constr to pr
o
duce constraints of typ
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
D
a
vid va
n
der Spoel
Fixed bug 417
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spo
e
l
Fi
x
es
m
ore misery in function ski
p
s
t
r, where
poin
t
ers
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David van der S
p
oel
Added two missing in
c
lude f
i
l
e
s
.
F
i
xed
h
orribl
e
coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David van der Spoel
Fixed
r
euse o
f
variable as temp vari
a
ble befo
r
e printing
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Dav
i
d
va
n
der Sp
o
e
l
F
ixed bug 487 according to provided patch
.
commit
|
commitdiff
|
tree
2010-08-03
Da
v
i
d van der Spoel
Fixed documenta
t
ion text ac
c
ording to bugzilla 486
commit
|
commitdiff
|
tree
2010-08-01
D
avi
d
van der
Spoel
Merge br
a
n
c
h 'release-4-5-patch
e
s' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Da
v
i
d van der Spoel
Moved pdb2
t
op
.
h from src/ker
n
el
to
i
nclude to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van d
e
r
S
poel
Renamed typ
e
n
a
me to my_typen
a
me in
index
.
c s
i
nce typena
m
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David
v
an der
S
p
o
el
Fixed compil
a
tio
n
issue c
o
r
r
espondin
g
to
b
ug 468
commit
|
commitdiff
|
tree
2010-07-13
Davi
d
van der Spoel
Fixed bu
g
466
by commenti
n
g o
u
t the offending lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d van de
r
S
p
oel
Merge branch 'master' of git
.
gromacs
.
o
r
g:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-08
Da
v
i
d
van d
e
r Spoel
A
d
ded b
o
ndedtypes section to r
t
p files
.
I
t
might
be
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
David van de
r
Spoel
Fixed include statements suc
h
that d
o
ubl
e
precision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
D
avid
v
an der Spoel
Merge
b
ranch 'master' o
f
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-02
David
v
an der
S
poel
Made removing pbc
non-stat
i
c
.
This aff
e
cts many analys
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David va
n
der
S
p
oel
Me
r
ge b
r
anch 'm
a
s
ter' of
git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Fixed bug
http://
b
ugz
i
ll
a
.
gromacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David
van d
e
r
Spo
e
l
Fi
x
ed http
:
//bugzil
l
a
.
gromacs
.
or
g
/
show
_
bug
.
cgi?
i
d=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David
v
an der
Spoel
Merge b
r
anch 'master'
of git
.
groma
c
s
.
o
rg:
g
romacs
commit
|
commitdiff
|
tree
2010-06-30
D
a
vid van der Spoe
l
Fixed
b
u
g in b-
f
actors
o
utput by g_confrms
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David v
a
n der Spoel
Added miss
i
ng argu
m
ent step to
t
rotter_updat
e
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid van der Spoel
Merge branch 'master'
o
f git
.
grom
a
cs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-06-27
David van
d
e
r
Spoel
U
p
d
a
t
ed CMa
k
eLists
.
txt i
n
ngmx directory to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van der Spoel
F
ix
e
d many issues regardi
n
g to comp
i
l
ati
o
n with C
+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der Spoel
Fixe
d
Makefile
.
am leading to warnings
.
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Fixed
m
ake_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
David va
n
der
S
p
o
el
Merge branch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-14
David van de
r
Spoel
Adde
d
more
f
ixes in comment tex
t
s
,
genero
u
sly pr
o
vided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
David van d
e
r Spoel
Fixed a lot o
f
spel
l
ing
er
r
ors in comments and do
c
u
me
n
tation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David v
a
n der Spo
e
l
Merge
b
ranch 'm
a
ster' of git
.
gro
m
ac
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-11
D
a
vi
d
van
d
e
r
Spoel
Fixed fo
r
ce field
f
iles fo
r
A
TP in
order to cl
e
a
r
b
ug
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d v
a
n d
e
r Spo
e
l
Merge branch 'master' of git
.
g
r
omacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Made
l
e
g
e
n
d more or
l
ess work in g_chi
.
Don't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van der
Spoel
F
ixed
SEGV in g
_
chi as descri
b
e
d in bug 4
3
0
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Ad
d
ed option -
n
opbc
t
o
g
_
rmsdist
i
n order t
o
f
ix
commit
|
commitdiff
|
tree
2010-06-10
David va
n
der Spoel
Pedanti
c
change in
t
he check whether a fi
l
ename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David v
a
n der Spoel
R
e
named some
programs to follow the g_ doct
r
ine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der S
p
oel
Cleane
d
up an
d
renamed files i
n
ngmx di
r
ect
o
ry to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
Renam
e
d some files i
n
a
r
ound
a
bout way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
Removed a
v
erage
.
c, t
h
at functionality is now
in
g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Fixe
d
strange ty
p
o in gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David
v
an
d
e
r Spoel
Moved warnin
g
messa
g
e in a
d
d_atomtype to b
e
printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David
v
an der Sp
o
el
Made x2top (very) slight
l
y functional again
.
Still
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
v
id van de
r
Spoel
Changed error message for settle p
r
oblems, suc
h
that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Added explicit angle in AC
E
dec
l
a
r
a
tio
n
in
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
an der Spoel
Fixed type in gmx_morph
.
c: efTRO
-> efTRX whic
h
lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David v
a
n der
Spoel
Fixed bug
3
96
.
In
f
a
ct
i
t
was
already fixed partly
.
commit
|
commitdiff
|
tree
2010-05-25
David
v
a
n
der S
p
o
e
l
Merge b
r
anch
'
master' of
git
.
gr
o
macs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-05-25
Da
v
i
d van der Spoel
Added
one more!
commit
|
commitdiff
|
tree
2010-05-21
David van der Sp
o
el
F
i
xed compilation w
a
rnings and removed spurious C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
David van der Spoel
Made
g_analyze co
m
pile
a
gai
n
, but ot link
y
et
.
commit
|
commitdiff
|
tree
2010-05-19
David van de
r
Spoel
M
erge bran
c
h 'mast
e
r
' of g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-19
David van
der Spoel
Added check
i
n
read_pdb for exis
t
e
n
ce of t_resinfo
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
David
v
an der Spoel
Added a
c
ool quo
t
e,
an
d
removed two
comma's in openmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Dav
i
d
va
n
der Spoel
M
e
rge branc
h
'
m
as
t
er'
of git
.
gro
m
a
c
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-05-16
David van der Sp
o
el
F
i
xed s
c
attering f
u
nction code
in g_rdf
.
A new f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-04-30
D
a
vid v
a
n der
S
poel
Added one
commit
|
commitdiff
|
tree
2010-04-04
David va
n
d
e
r Spoel
A
d
ded one
.
commit
|
commitdiff
|
tree
2010-04-04
D
avi
d
van der Sp
o
el
M
e
rge
branch 'master
'
of
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-12
Dav
i
d van der Spoel
Merge br
a
nch 'master' of git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-12
David van
d
er Spoel
Added flush afte
r
wri
t
ing to debug file
commit
|
commitdiff
|
tree
2010-02-14
D
a
vid van der Spoel
Added f
u
nction to
increase t
h
e array sizes i
n
a
t_atoms
.
.
.
commit
|
commitdiff
|
tree
2010-02-13
Dav
i
d van der Sp
o
el
R
eplaced so
m
e strc
p
y by strncpy to avoid ove
r
flows
.
commit
|
commitdiff
|
tree
2010-02-06
David van der Spoel
Replaced
tw
o
str
c
py by
strncpy in
p
dbio
.
c to prev
e
nt
.
.
.
commit
|
commitdiff
|
tree
2009-12-14
David v
a
n der Spo
e
l
Chang
e
d a
t
omnumbe
r
for OS (opls_179, opls_180) to 8
.
.
.
commit
|
commitdiff
|
tree
2009-12-07
David van der Spoel
Merge br
a
nch
'
master' of git
.
gro
m
a
cs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2009-12-07
David van der
S
poel
Up
d
ated
commit
|
commitdiff
|
tree
2009-12-01
David van
der
S
poel
A
dded
i
n
clude/vmdio
.
h to th
e
in
s
tallable
h
e
ad
e
rs due
.
.
.
commit
|
commitdiff
|
tree
2009-11-15
D
a
v
id v
a
n
der Spo
e
l
Added check
f
or chdir return value
.
commit
|
commitdiff
|
tree
2009-11-10
D
avi
d
van der
Sp
o
el
Ad
d
ed
2!!!
commit
|
commitdiff
|
tree
2009-09-18
David v
a
n
de
r
S
poel
Added a
lot of help text
commit
|
commitdiff
|
tree
2009-09-18
D
av
i
d van der
S
poel
R
e
m
oved confusing --d
i
sable-nice
commit
|
commitdiff
|
tree
2009-09-18
David van der Spoel
Mer
g
e branch '
m
as
t
er' of git
.
gr
o
ma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2009-09-18
Da
v
id van d
e
r Spoel
Added functional
i
t
y
t
o
cha
n
ge directories and
b
a
ck
.
.
.
commit
|
commitdiff
|
tree
2009-09-18
David van d
e
r Spoel
Fixed compilation issue
.
commit
|
commitdiff
|
tree
2009-09-15
Dav
i
d van
de
r
Spo
e
l
M
a
de regul
a
r h
i
stogram for g_
c
lustize to repres
e
nt
.
.
.
commit
|
commitdiff
|
tree
2009-09-14
David van der S
p
o
e
l
Merge branch 'master' o
f
g
i
t
.
gro
m
ac
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2009-09-14
David van der Sp
o
el
M
ade st
a
tistics work
w
ith only 1 d
a
ta point
commit
|
commitdiff
|
tree
2009-08-27
D
avid van der Spoel
Merge branch 'master'
of g
i
t
.
g
r
omacs
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2009-08-27
Davi
d
van der Spoel
Made thread stuff optiona
l
commit
|
commitdiff
|
tree
2009-08-27
David van der S
p
oel
Ad
d
ed missing file
n
am
e
commit
|
commitdiff
|
tree
next