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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-10-28
David
v
an
d
e
r Spoel
Merge branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David van der Spoel
Merge branch
'
release
-
4
-
5-patc
h
es' of gi
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David van der
Sp
o
e
l
Fixed compilation issues with C99 co
m
pat
i
b
i
lity
.
commit
|
commitdiff
|
tree
2010-10-07
David van der Spo
e
l
Fixes and small
a
ddi
t
ions to g_wham
,
due to Joche
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David
v
an
d
e
r Spoel
Re-ad
d
e
d
g_
k
in
e
tics
t
o
src/to
o
l
s
/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
Davi
d
van
der
Spoe
l
A
dded sof
t
ware
-
rel
a
ted
quote
commit
|
commitdiff
|
tree
2010-09-24
D
a
v
i
d
v
an der Spoel
Upd
a
ted to
r
eflect
b
ug 557
.
commit
|
commitdiff
|
tree
2010-09-20
D
avid van de
r
Spoel
Merge branch 'release-4-5-patches' of git@gi
t
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Dav
i
d van der Spoel
Fixed b
u
g http://bu
g
z
i
l
la
.
gromacs
.
o
rg/show
_
bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David van der Spoel
Correc
t
e
d
n
a
me
of one of the developers listed in hea
d
er
.
commit
|
commitdiff
|
tree
2010-09-14
Da
v
id van de
r
Spoel
F
i
xed bug 55
3
by
c
h
eckin
g
w
hethe
r
an a
t
om name
i
s longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David van der Spoel
Fixed demo to work with new pd
b
2gmx th
a
t
requires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Da
v
id v
a
n der Spoel
M
a
de g
e
nrestr
-constr to pr
o
duce constraints of t
y
pe
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David v
a
n der
S
p
oel
F
i
x
e
d bug 417
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Fixes mo
r
e m
i
sery in function skipstr,
w
h
e
r
e pointers
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David
v
an d
e
r Spoel
Added two missi
n
g inclu
d
e files
.
Fixed horrib
l
e coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David van der Spoel
Fixed reuse of varia
b
le as t
e
mp va
r
i
a
ble
b
efore printi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David van der S
p
oel
Fixed bug 487 acco
r
d
i
n
g to
provid
e
d pa
t
ch
.
commit
|
commitdiff
|
tree
2010-08-03
Davi
d
van der Spoel
Fixed
documenta
t
i
o
n text acc
o
rding to bugzi
l
la
4
86
commit
|
commitdiff
|
tree
2010-08-01
David van der Spo
e
l
Merge branch 'release-4-5-patc
h
es' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
D
avid va
n
de
r
Spoel
M
o
v
ed pdb2t
o
p
.
h from s
r
c
/
k
e
rnel to in
c
lude to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David va
n
der Spoel
Renamed typenam
e
to my_typename in index
.
c since
t
y
pename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David
van der
Sp
o
el
Fixed
c
ompilation issue corresponding to bug
4
6
8
commit
|
commitdiff
|
tree
2010-07-14
David van der Spo
e
l
Fixed bug 467 realting
t
o pdb2gmx output of the water
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
Da
v
id van der Spoe
l
Adde
d
citation for scatterin
g
factor
s
.
Us
e
d
in g_rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David
van d
e
r Spoel
A
dd
e
d
m
ore atoms t
o
the scattering
f
actor da
t
a file
.
commit
|
commitdiff
|
tree
2010-07-14
Davi
d
van der Spoel
F
i
x
e
d
bug 4
6
2
.
pd
b
2g
m
x
should now produce the co
r
rect
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
D
a
vid
van de
r
Spoel
F
ixed bug
466 by comme
n
t
ing out the offending lin
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David van der Spoel
M
e
rge branch 'master' of git@
g
it
.
g
r
omacs
.
org:gr
o
m
a
cs
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d
va
n
der
S
p
oel
Added initializa
t
ion
o
f
pbc struct in genborn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
D
av
i
d van der Spoel
Ad
d
ed initialization
o
f pb
c
structu
r
e before calc_gb_for
c
es
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David
v
an der Spoel
Merg
e
branch 'mas
t
e
r
' o
f
git
.
gro
m
acs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-08
D
a
vi
d
v
an der Spoel
Added b
o
nde
d
types section
to rtp
f
iles
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
Spoel
Removed possible SEGVs in rm
p
bc in case ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
S
poel
Mer
g
e branch 'master' of git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
D
a
vid
v
a
n
d
e
r Spoel
Merge branch
'
master' of git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-07
David van der Spoel
Fixed mise
r
a
b
le bug in commrec
.
h where an
i
nt array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David van
der Spoel
Fixed bug in g
m
x
_
su
m
f_com
m
whe
r
e
a
doubl
e
a
rray was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Davi
d
v
a
n
d
er
S
p
oel
Merge bran
c
h 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
David van der Spoel
M
erge branch 'ma
s
ter'
of git
.
gromacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2010-07-05
David van der Spoel
Added sfactor
.
dat
to t
h
e insta
l
lati
o
n ta
r
gets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
D
a
vid van d
e
r Spoel
Fixed
include statements su
c
h that d
o
uble
precis
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Davi
d
v
a
n
d
e
r
Spoel
Merg
e
branch
'
maste
r
'
of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
D
a
vid van
der Spoel
Mad
e
removing pbc n
o
n-static
.
Thi
s
affects man
y
an
a
lysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Da
v
id
van der Spoel
Merge
b
ran
c
h 'master' of
g
it
.
grom
a
c
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-02
David v
a
n der Spoe
l
Fixed
b
ug http
:
//bugzil
l
a
.
g
r
o
macs
.
org/show
_
bug
.
c
g
i
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van
der Spoe
l
Fi
x
ed http://b
u
gzilla
.
gromacs
.
org/s
h
ow
_
bug
.
c
g
i?id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Sp
o
el
M
erge
b
r
anch '
m
a
ste
r
' of git
.
g
r
omacs
.
o
rg:gro
m
a
c
s
commit
|
commitdiff
|
tree
2010-06-30
David van der Spoel
Fixed bug
in b-fact
o
r
s output by
g_confrms
.
T
h
ey
were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
van der Spoel
A
dde
d
mi
s
sing argument s
t
ep to trotter_u
p
date
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Davi
d
van
d
er
Spoel
Merge
branch 'master' of git
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-27
David v
a
n der Spoel
Updated CMakeLis
t
s
.
txt i
n
ngmx direct
o
r
y
to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid van der
Spoel
Fixed many issues regarding to
compilation wit
h
C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der
S
p
oel
Fixed Makefile
.
am l
e
adin
g
to wa
r
n
ings
.
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van der Spoel
Fixed make
_
edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van der Spo
e
l
M
e
rge branch 'master' of g
i
t
.
gromacs
.
o
r
g:groma
c
s
commit
|
commitdiff
|
tree
2010-06-14
D
a
v
i
d
van der Spoel
Add
e
d mor
e
f
i
x
es in comment
t
exts, ge
n
e
rously provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Davi
d
va
n
d
er Sp
o
el
Fixed
a lot o
f
spelling
errors in comm
e
nts
and documentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
D
avid va
n
d
e
r S
p
oel
Merge branch
'ma
s
t
e
r' of
g
it
.
g
romacs
.
org:g
r
o
m
a
cs
commit
|
commitdiff
|
tree
2010-06-11
David van der
Spo
e
l
F
i
xed force
field files
for ATP in order to clear bug
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
M
e
rge branch 'master' of
g
it
.
gromacs
.
o
rg
:
gromacs
commit
|
commitdiff
|
tree
2010-06-10
David va
n
der Spoel
Made
l
egend
m
ore or le
s
s work
i
n g
_
chi
.
D
o
n't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Da
v
id va
n
der Spo
e
l
Fixed SEGV in g_c
h
i as described
in
b
ug
4
30
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d van
der Spoel
Added opti
o
n -nopbc to g_rmsdist in order to fix
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Pedantic change in the chec
k
whet
h
er a filename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Da
v
i
d
van de
r
Spo
e
l
Re
n
amed some program
s
t
o
follow t
h
e g_ doctrine:
l
uck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spo
e
l
Cleaned up and rena
m
e
d
files
in n
g
m
x
direc
t
o
r
y
t
o
be
t
ter
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
id
van der Spoel
Renam
e
d
som
e
fi
l
es
in a roundabout
way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid
v
an d
e
r
S
p
oel
Removed averag
e
.
c, that functi
o
nalit
y
is now
i
n
g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d
v
an der
S
poel
F
i
xed
strange typo in gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
Dav
i
d
v
an der Sp
o
el
Mov
e
d warning message in ad
d
_atomtype to be printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David
v
a
n
der Spoel
Made
x
2top (very) slightly funct
i
onal again
.
Still
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
an de
r
Sp
o
e
l
Changed error mes
s
age for
settle prob
l
ems, su
c
h that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
A
dded explicit
a
ngle in
A
C
E
declaration
in gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
v
id van der Spoel
Fixed type in gmx_m
o
rph
.
c:
efTRO -> efTRX which
l
ea
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spoel
Fi
x
ed
bug 39
6
.
In fact it was already fixed partly
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
an
d
er Spoel
Fixed bug 401 by
i
mpl
e
me
n
ting the propo
s
ed patch tha
t
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
d
er Sp
o
e
l
F
ixed bug 381 by adding the number of
the fi
r
st a
t
om
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
F
i
x
e
d bug 34
9
.
The file made with the
-
vis option h
a
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David va
n
der Spoel
Me
r
ge b
r
anch 'm
a
ster' of git
.
grom
a
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d
v
an der Spoel
Re
m
ove
d
opt
i
on CAN_DT from g_msd, since
it can
n
ot handle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
de
r
Spoe
l
Incre
a
s
ed buf
f
er size
f
o
r
r
eading
i
n a w
h
ole file at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
David van der Spoel
M
e
rge
bran
c
h 'master'
o
f git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-25
Dav
i
d van der S
p
oel
A
d
ded one more!
commit
|
commitdiff
|
tree
2010-05-24
David v
a
n de
r
Spoel
Removed
C
++ st
y
l
e
comments in mdrun
.
commit
|
commitdiff
|
tree
2010-05-21
David van
d
er Spoel
Fixed compilation warning
s
and remove
d
spurious C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
D
a
v
i
d va
n
der Spoel
Add
e
d 1
commit
|
commitdiff
|
tree
2010-05-20
Da
v
i
d
van
d
e
r Spoel
Made g_a
n
alyze compile
a
ga
i
n, bu
t
ot
l
ink y
e
t
.
commit
|
commitdiff
|
tree
2010-05-19
Davi
d
van der
S
p
oel
M
e
rge b
r
a
n
c
h 'm
a
ster'
o
f g
i
t
.
g
r
o
macs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-05-19
David van der Spoel
Added c
h
eck
i
n r
e
ad_pdb for exi
s
tenc
e
o
f
t
_resinfo
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
Dav
i
d v
a
n
der
S
poel
Added a cool qu
o
te
,
a
n
d
rem
o
ve
d
two comma's in openmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van
d
er Spoel
Mer
g
e b
r
an
c
h 'master' of
git
.
g
romacs
.
or
g
:gr
o
m
acs
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
Fixed scatte
r
in
g
functio
n
code in g_rdf
.
A new file
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Dav
i
d
van
der Spoel
Ad
d
ed multi reg
r
ession analysis to g_analy
z
e
.
See in
f
o
.
.
.
commit
|
commitdiff
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tree
2010-05-16
D
avid van der Spoe
l
Fixed compi
l
ation issue in
geminate
.
c due to non-defined
.
.
.
commit
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commitdiff
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tree
2010-05-16
David
v
an
der
Spoel
Merge branch 'master' o
f
git@git
.
grom
a
c
s
.
org:gromacs
commit
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commitdiff
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2010-05-12
Da
v
id van der Spoe
l
Merge branch
'
m
a
ster' of gi
t
.
g
rom
a
cs
.
or
g
:gro
m
acs
commit
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commitdiff
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tree
2010-05-12
David van de
r
Spoe
l
Delt
e
d two more superfl
u
ous files
commit
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commitdiff
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2010-05-11
Da
v
id van der Spoel
Clea
n
ed up in top directory
.
Mov
e
d a
few old itp files
.
.
.
commit
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commitdiff
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2010-05-11
Da
v
id van der S
p
o
el
Moved phosphate files into
gmx
.
ff d
i
rector
y
.
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