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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2011-04-10
David va
n
der
Spo
e
l
Merge br
a
nch
'
release-
4
-5-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
David
van der Spoel
Added g_hydord
e
r
.
1 man page
.
commit
|
commitdiff
|
tree
2011-04-06
Dav
i
d
va
n
der Spoel
F
i
x
e
d header for gmx_
c
onect_init
commit
|
commitdiff
|
tree
2011-04-04
D
a
vid
van d
e
r Spoel
Mer
g
e branch
'
rel
e
ase-4
-
5-p
a
tches' of
g
i
t
@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
David van de
r
S
p
o
el
Rem
o
ved
s
u
p
erfluous file
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
van
d
er Spoel
Made
new pro
g
rams
c
ompile
with gcc
-pedantic
.
commit
|
commitdiff
|
tree
2011-04-04
David van der Sp
o
el
New en
t
ry
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
van der Spoel
Ad
d
ed 1 analysis tool manual
.
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n der Spo
e
l
Merge branch 'release-4-5
-
patches' in
t
o
o
rderp
a
rm
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
van de
r
Spoel
Late
s
t fixes from Bjorn
S
t
e
en
Saethre
commit
|
commitdiff
|
tree
2011-03-24
David van der
Spoel
A
d
ded Bjorn's code
,
implemented
runni
n
g av
e
rage filte
r
i
n
g
.
commit
|
commitdiff
|
tree
2011-03-05
David van der Spoel
Me
r
ge branch 'rel
e
ase-4-
5
-pa
t
ches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David va
n
der Spoel
Fi
x
ed SEGV
i
n
e
n
econv
when using the -e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
Fixed mor
e
PBC and i
n
dexing
s
t
u
ff
.
commit
|
commitdiff
|
tree
2011-01-30
David van der
S
poel
F
i
x
e
d typo
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
van der Spoel
Merge branch 'release-
4
-
5
-patc
h
es' int
o
orderp
a
r
m
commit
|
commitdiff
|
tree
2011-01-29
David
van der Spoel
Me
r
ge branch
'
relea
s
e-4-5-patch
e
s'
of git@git
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
David van
der Sp
o
el
Added
c
ode
i
n
g
_n
m
eig to compute the q
u
antum c
o
r
r
ections
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
Dav
i
d va
n
der Spoel
Merge bra
n
c
h
'release-4
-
5-patches' of git
@
git
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van der Spoel
Fixed
b
ug
678 which was due to
calling gmx_fatal without
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
David
v
a
n
der Spoel
Merge branc
h
'releas
e
-4-
5
-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van der
S
p
o
el
Added w
a
rning i
n
g_dipoles
commit
|
commitdiff
|
tree
2010-12-23
Da
v
i
d
va
n
de
r
Spoel
Fixed
bug in s
t
atisti
c
s
w
hich did not allow fitting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
avid
v
an der Spoel
Merge bran
c
h 'releas
e
-4-5-
p
atches'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David va
n
der Spoel
Added
1 quote
.
commit
|
commitdiff
|
tree
2010-12-09
D
av
i
d van de
r
Spoel
Added
fatal
e
rr
o
r for when
p
e
o
ple use energy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
David van der S
p
oel
F
ixed bu
g
z
illa 616 ab
o
ut
formatting in th
e
h
e
l
p te
x
t
.
commit
|
commitdiff
|
tree
2010-11-26
David van der Spoel
Fixed SEG
V
bug in g_sham
.
commit
|
commitdiff
|
tree
2010-11-18
David van der
S
poel
Made
p
rinti
n
g in ch
e
c
k
_multi_init conditional,
d
ependi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
David
v
an der Spoel
Fixed
b
u
g 608
b
y
throwing a f
a
t
al error in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
David
van der Spoel
Merge
b
ranch 'release-
4
-
5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
D
a
vid van der
S
p
oel
M
erge branc
h
'r
e
l
e
a
se-4-5-patch
e
s' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David va
n
d
er Spo
e
l
F
i
xed compilation issu
e
s
with C9
9
compatibility
.
commit
|
commitdiff
|
tree
2010-10-07
David van der S
p
oe
l
F
i
x
e
s
a
nd small add
i
tions to g_wham, due to
J
ochen
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David van der Spoel
Re-added g_k
i
netics t
o
src/tool
s
/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
David
van der S
p
oel
A
d
ded
s
oftware
-
r
e
lated qu
o
te
commit
|
commitdiff
|
tree
2010-09-24
David van d
e
r Spoel
Upda
t
ed
t
o reflect bug 557
.
commit
|
commitdiff
|
tree
2010-09-20
D
a
vid v
a
n
de
r
Spoel
Merg
e
br
a
n
ch 'release-4-5-patche
s
' of g
i
t
@
g
it
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
David van der
S
p
oel
Fi
x
ed bug htt
p
:
/
/b
u
gzi
l
la
.
groma
c
s
.
org/show_bug
.
cg
i
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David v
a
n der Spoel
C
orrected name o
f
one of the develop
e
rs listed in header
.
commit
|
commitdiff
|
tree
2010-09-14
D
a
vi
d
v
a
n
de
r
S
p
oel
Fixe
d
b
u
g 553
by che
c
king whether an
atom nam
e
is longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David van de
r
S
poel
Fi
x
ed de
m
o to work with n
e
w pdb2gmx that r
e
quires t
w
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David van der Spoe
l
Ma
d
e g
e
nrestr
-
constr to pro
d
uce constra
i
nts of t
y
pe
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Davi
d
v
an der
Spoel
Fixed bu
g
4
1
7
.
commit
|
commitdiff
|
tree
2010-08-19
D
a
vid van der Spoel
F
i
xes
more misery in functio
n
ski
p
str
,
where
pointers
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Dav
i
d van der Spoel
Added two
m
i
ssing
i
ncl
u
de file
s
.
Fixed horrible co
d
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David van
d
er Spoel
F
ixed
r
eu
s
e of variable as temp variable bef
o
r
e
prin
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
D
a
vid van der Spoel
F
ixed bug 487 ac
c
ording to pr
o
vided
patch
.
commit
|
commitdiff
|
tree
2010-08-03
David v
a
n
d
er Spoel
F
ix
e
d documentation text
accord
i
ng to bugzi
l
la 486
commit
|
commitdiff
|
tree
2010-08-01
Da
v
id van der Spoel
M
erge
branc
h
'release-4-5-pat
c
hes' of git
.
g
rom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David
v
an de
r
Spoel
Moved pdb2top
.
h from
s
r
c/kernel to incl
u
de to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van der Spoel
R
enamed typename to
m
y_type
n
ame i
n
index
.
c since typename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David van der Spoel
F
i
xed compilat
i
on issue correspo
n
ding to bug 468
commit
|
commitdiff
|
tree
2010-07-14
Dav
i
d van der Spoel
Fixe
d
bug 467 realting to pdb2g
m
x outpu
t
of
the water
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
Added citation f
o
r scattering factors
.
Used in g_r
d
f
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
Added
mor
e
atoms to the scattering factor
d
a
ta file
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
F
i
x
e
d bug 462
.
pdb2gmx sho
u
ld no
w
pro
d
uce the corr
e
ct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
David van der Spoel
Fixed bug 466 by c
o
mment
i
n
g
out the offe
n
ding li
n
es
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d
v
an der Spoel
M
e
r
ge branch
'
mast
e
r'
o
f git
@
git
.
grom
a
cs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-12
David va
n
d
er Spoel
Added initi
a
lization of
p
bc stru
c
t in genbo
r
n
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
David van der Spoel
Added in
i
t
i
alizati
o
n of pbc
structure b
e
fore calc
_
gb_forces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David
v
an der Sp
o
el
Merg
e
branc
h
'master'
o
f
g
it
.
gromacs
.
org:gr
o
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-08
David v
a
n der Spoel
Added bondedtypes section to rtp files
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David
v
an der Sp
o
el
Remov
e
d possible SEGVs i
n
rm
p
bc in case ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d
va
n
d
er Spoel
Merge branch '
m
a
ster' of gi
t
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-07
David van der Spoel
Merge branch
'
master'
of git
.
gr
o
macs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-07
D
a
vid van der Spoel
F
ixed miserable bu
g
i
n
commrec
.
h where an
i
n
t arra
y
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David
van
de
r
Spoel
Fi
x
e
d
bug
in gmx_s
u
mf_c
o
m
m
w
h
e
r
e
a double arr
a
y was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David va
n
d
er Spoel
Merge b
r
a
n
ch
'master' of git
.
g
r
om
a
cs
.
o
r
g:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-05
David van der Spoel
Merge branch
'
master' of git
.
g
r
omac
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-05
David van de
r
Spoel
Added
s
f
acto
r
.
dat
t
o t
h
e inst
a
l
l
ati
o
n
t
arge
t
s in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
David van
d
er Spoel
Fix
e
d i
n
clude stat
e
ments
such that double pre
c
ision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Dav
i
d v
a
n
der
Spoel
Merg
e
b
r
anch 'm
a
s
t
er' of git
.
gromacs
.
o
r
g:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-02
David van
d
e
r Spo
e
l
Made
removing pb
c
non-static
.
This affects
m
a
ny a
n
alysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Dav
i
d van der
Spoel
Merge
b
r
anc
h
'master' of
g
it
.
g
r
omacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-02
David van der
Spoel
Fi
x
ed bug http://bu
g
z
illa
.
g
romacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
Dav
i
d van der Spoel
Fi
x
ed http://
b
ugzilla
.
g
r
omacs
.
o
r
g
/
show_bug
.
cgi
?
id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David va
n
d
e
r Spoel
Merge branch 'master' of git
.
gr
o
ma
c
s
.
o
r
g:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-30
D
a
vid v
a
n der
Sp
o
el
Fixed bug in b-factors outp
u
t
b
y
g_confrms
.
The
y
were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van
der
Spoel
Ad
d
e
d
missing
a
rgument step to trotter_u
p
date
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van
der Spoel
Mer
g
e br
a
nch 'mas
t
er'
of gi
t
.
g
r
omacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-27
Dav
i
d van de
r
Spoe
l
Up
d
ate
d
CMakeLists
.
txt
i
n ngmx directory
t
o
exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
v
an der Sp
o
el
Fi
x
ed many iss
u
es regarding to compilation with C
+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van
der Spo
e
l
Fixed
M
akefile
.
am lead
i
ng to wa
r
nings
.
commit
|
commitdiff
|
tree
2010-06-14
David van der Sp
o
el
Fixed make_e
d
i
.
c
commit
|
commitdiff
|
tree
2010-06-14
D
avid
van
d
er Spoel
Merge branch 'mas
t
er' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van der Spoel
Add
e
d
m
ore fixes in comme
n
t
t
e
xts,
generously provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Dav
i
d van der
S
poel
Fixed
a
lot of spelling
errors in comments and documentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
Da
v
id van der
Spoel
Merge
branch 'master' of git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David
v
an der Spoel
Fixe
d
f
o
rce fie
l
d
f
il
e
s for ATP in order to clear bu
g
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Merge b
r
anch 'ma
s
ter' of git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-06-10
David van d
e
r Spoel
Made legend mor
e
or less work
in g_chi
.
Don't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der
Spoel
Fixed SEGV in g_chi as described
i
n bu
g
430
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
v
an der
S
poel
Adde
d
option -nopb
c
to g_rmsdist in order to fix
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der
S
p
oel
Pedantic ch
a
nge in
t
he check wh
e
ther a filena
m
e
is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der Spoel
Renamed so
m
e programs
t
o follow the g_ doctr
i
ne: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van
der Spoel
Cleaned
u
p and
r
ename
d
f
iles in
ngmx d
i
re
c
tor
y
to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van de
r
Spoel
Renamed some files in a roundabout way to adher
e
to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
R
e
moved average
.
c
,
that
f
unctionalit
y
is
now in g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vi
d
van der
S
poe
l
Fixed stran
g
e
typo in gmx_dih
.
c
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