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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-10-28
David
van der Sp
o
el
M
e
rge branch 'rel
e
ase-4-5-pa
t
ches' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
D
a
vid van der Sp
o
e
l
Merge
b
ranch 'release-4-5-
p
atches
'
of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
Dav
i
d van
d
e
r
Spoel
Fixed
comp
i
la
t
ion
i
s
sues with
C99 compa
t
ib
i
lit
y
.
commit
|
commitdiff
|
tree
2010-10-07
David
v
an der Spoel
F
i
xes and small
additio
n
s to g_wham, due
t
o
Joche
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
Davi
d
va
n
der
S
poel
R
e-add
e
d g_kin
e
tics to sr
c
/to
o
l
s
/
Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
Da
v
id van der Spoel
Added software-related quote
commit
|
commitdiff
|
tree
2010-09-24
D
avid
van der
S
poel
Updat
e
d
to re
f
l
ect bu
g
557
.
commit
|
commitdiff
|
tree
2010-09-20
D
avid
v
an der Spo
e
l
Merge branch 're
l
e
a
se
-
4
-
5-patches' of git@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Davi
d
van der Spoel
Fixed bug h
t
t
p://bugzilla
.
gro
m
acs
.
org/show_bug
.
cg
i
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David van der Spoel
Corrected name o
f
o
n
e of the developers list
e
d in header
.
commit
|
commitdiff
|
tree
2010-09-14
David van der Spoe
l
Fixed bug 553
b
y checking wheth
e
r an ato
m
name is l
o
nger
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
Da
v
id va
n
der Spoel
Fixed
d
em
o
to work wi
t
h new
p
db2
g
mx that requi
r
es tw
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David van
d
er Spoel
Made ge
n
restr -cons
t
r to produce constraints of type
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David van der
S
poel
Fixed b
u
g 4
1
7
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Fixes more
m
isery
i
n
fun
c
tion
skip
s
tr, where pointers
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David va
n
der
S
poel
Ad
d
ed two
m
issing
include files
.
F
ix
e
d horrible coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David van d
e
r Spoel
F
i
xed reuse of variable as t
e
mp va
r
i
a
ble before printing
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Da
v
id van der Spoel
Fix
e
d bug 4
8
7
accordin
g
to p
r
ovided patch
.
commit
|
commitdiff
|
tree
2010-08-03
David
van
der S
p
o
e
l
Fi
x
ed docum
e
ntation
text
according to b
u
g
zilla 486
commit
|
commitdiff
|
tree
2010-08-01
David
v
an de
r
Spoel
Merge
b
ranch 'rele
a
se-4
-
5-patc
h
es' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David van der S
p
oel
Mo
v
e
d
pdb2
t
op
.
h
f
r
o
m src
/
ker
n
e
l
t
o include to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van
d
er
Spoel
Renamed
t
y
pename
t
o
m
y_typena
m
e in index
.
c since t
y
pename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
Dav
i
d van der Spoel
F
i
xe
d
compilation issue corres
p
o
ndin
g
t
o bug
4
68
commit
|
commitdiff
|
tree
2010-07-14
David
v
a
n
der Spoel
Fix
e
d
b
ug 467 realting
t
o pdb2gmx output of the wa
t
er
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spo
e
l
Added citation for s
c
a
t
t
ering factor
s
.
Used in g_
r
d
f
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van de
r
Spoel
Add
e
d more
atoms to th
e
scat
t
ering fac
t
o
r
d
a
t
a file
.
commit
|
commitdiff
|
tree
2010-07-14
Dav
i
d van der
S
p
oel
Fixed bu
g
46
2
.
pdb2gmx s
h
o
uld now p
r
oduc
e
th
e
co
r
rect
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
D
a
vid van der Spo
e
l
Fix
e
d bug
4
66 b
y
co
m
menting out the offending
l
ines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David
van der Spoel
Mer
g
e branc
h
'master' of g
i
t@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-12
D
a
vid van der
Spoe
l
Added initia
l
ization of pbc
s
truct in genborn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
David van de
r
S
p
oel
Ad
d
e
d
i
n
itialization o
f
pbc structure
b
ef
o
re calc_gb_forces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
Spoel
Merge branch 'm
a
st
e
r' of git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-08
David
van der Spoe
l
Add
e
d
b
ondedtypes section t
o
rtp
f
iles
.
It m
i
ght b
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d va
n
der Spoel
Rem
o
v
e
d
possi
b
le
S
EGVs in rmpb
c
in case e
P
BC =
N
o
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d van der Spoe
l
Merge br
a
n
c
h 'master' of git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Dav
i
d
v
an der Spoel
Merge
b
ranch 'master' o
f
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Da
v
id van
d
er Sp
o
el
Fixed mise
r
able bug
in commrec
.
h where an int array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Davi
d
v
a
n
d
e
r Spoe
l
Fixed bu
g
in g
m
x_sumf
_
comm where a double
a
rray
w
as
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Davi
d
van der Sp
o
el
Merge br
a
nch 'master' o
f
git
.
gromacs
.
org
:
gro
m
acs
commit
|
commitdiff
|
tree
2010-07-05
D
avid van d
e
r S
p
oel
M
erge branc
h
'm
a
ster' of
git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
David van
d
er
S
poel
Added
sf
a
c
t
or
.
d
at to the installation targets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
D
a
v
id v
a
n der Spoel
Fixed inclu
d
e state
m
ents such that double p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David
v
an der
Spoel
Merge branch 'master' of git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Made removing
p
bc non-
s
tatic
.
This
a
ffects many analysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Merge branch 'master' of git
.
groma
c
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-02
Davi
d
va
n
de
r
Spoel
F
ixed bug
h
ttp://bugzilla
.
gromacs
.
org/show_bug
.
c
g
i
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Spoel
Fixe
d
ht
t
p
://
b
ugzilla
.
g
r
om
a
cs
.
org/show_bug
.
cgi?id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Spo
e
l
Me
r
ge branch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-30
David van der Spoel
F
ixed
bug in b
-
factors o
u
t
p
ut by g_confr
m
s
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van der Spoel
Added mi
s
sing argument step to
trotter_u
p
date
.
Ho
w
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der
Spoel
Merge b
r
anch 'master' of gi
t
.
g
r
o
m
acs
.
or
g
:
gromacs
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid
van der Spoel
Upda
t
ed
CMakeList
s
.
txt in ngmx di
r
ectory
t
o
e
xclu
d
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid van
d
er S
p
oel
Fixed many i
s
s
ues regardi
n
g to
compil
a
tion with C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
D
a
v
id van der Spoel
Fixe
d
Makefile
.
a
m
leading to warnin
g
s
.
commit
|
commitdiff
|
tree
2010-06-14
Da
v
i
d v
a
n der
Spo
e
l
F
ixed make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
Dav
i
d va
n
de
r
Spoel
Merge branch 'maste
r
' of git
.
gromac
s
.
org:g
r
omac
s
commit
|
commitdiff
|
tree
2010-06-14
David van de
r
Spo
e
l
A
d
ded
more fixes in com
m
ent t
e
xts,
g
en
e
rously pro
v
ide
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Davi
d
van
d
er Spo
e
l
F
i
x
e
d a
lot
of spe
l
ling
e
rrors in comments and do
c
u
m
entation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
D
a
vid
v
an der Spoel
Merge bra
n
ch
'
master' of git
.
g
romacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
Fixed force field fi
l
es for ATP i
n
order to
c
l
ear
b
ug
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
va
n
der
Spoel
M
e
rge branch 'm
a
ster' of
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-10
D
avid van
der Sp
o
el
Made legend more or les
s
work in g_chi
.
D
o
n't
k
n
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van de
r
Spoel
Fixed SEG
V
in
g_c
h
i as des
c
ribed in
bug 43
0
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Added opti
o
n -nopb
c
to g_rmsdist
in
o
rd
e
r to f
i
x
commit
|
commitdiff
|
tree
2010-06-10
David va
n
d
er Spoel
Pe
d
antic
c
ha
n
ge in th
e
check wh
e
ther
a filename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van der Spoel
Renamed some pr
o
grams to fol
l
ow the g
_
doctri
n
e: lu
c
k
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
C
lea
n
e
d up and renamed
f
iles in ngmx d
i
rectory to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van
d
er S
p
oel
Renamed some files i
n
a roundabout way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Removed a
v
erage
.
c, that functiona
l
i
ty
i
s no
w
in
g
_ana
l
yze
.
commit
|
commitdiff
|
tree
2010-06-10
David va
n
der Spoel
F
i
xed str
a
nge typ
o
in gm
x
_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David v
a
n der S
p
oel
M
ove
d
warn
i
n
g message in
add_atomtype
t
o
be pr
i
nted
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David van der Spoel
Made x2top (very
)
slig
h
tl
y
function
a
l
a
gain
.
Stil
l
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
van
der Spo
e
l
Changed
error message for settle problems,
such that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
v
i
d va
n
de
r
S
p
oel
Add
e
d ex
p
licit angle i
n
AC
E
d
ecl
a
ration in gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spoel
Fixed type
i
n
gmx_
m
orph
.
c: efTRO
-
> ef
T
RX
which lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoe
l
Fi
x
ed
b
u
g 39
6
.
In fact it was alr
e
a
d
y fixed part
l
y
.
commit
|
commitdiff
|
tree
2010-06-02
David
van der Spoel
Fixed bug 401 by implem
e
n
t
i
ng th
e
propo
s
e
d patch
that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid van der Sp
o
e
l
Fixed bug 381
b
y adding th
e
number
o
f the first ato
m
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fixed bug 349
.
The
file
ma
d
e with the
-vis option has
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d
van der Spoel
Merge bra
n
ch 'master' of g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spoel
Removed option CAN_DT from g_msd, since it cannot handle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
van de
r
S
poel
Increased buffer size f
o
r
reading in a who
l
e
f
i
l
e at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Da
v
id v
a
n
d
er Sp
o
el
Mer
g
e branc
h
'master'
o
f git
.
gr
o
macs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2010-05-25
David v
a
n
der Spoel
A
d
d
ed one more!
commit
|
commitdiff
|
tree
2010-05-24
David van
der
S
p
oe
l
Removed C+
+
style comm
e
nts in mdr
u
n
.
commit
|
commitdiff
|
tree
2010-05-21
David van d
e
r Spoel
F
ix
e
d com
p
i
lation warnings
a
n
d removed spurious C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
David
van der
S
p
oel
Added 1
commit
|
commitdiff
|
tree
2010-05-20
David van der Spoe
l
Mad
e
g
_analyze comp
i
le ag
a
in,
b
ut ot link yet
.
commit
|
commitdiff
|
tree
2010-05-19
David van
der S
p
oel
Merge branch '
m
a
s
ter
'
of git
.
groma
c
s
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-05-19
David van der Spoel
Ad
d
ed che
c
k
i
n read_pdb
for existence of t_resinf
o
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
David van der Spoel
A
d
de
d
a cool quote, and removed two comma's in openm
p
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
D
a
vid v
a
n der Spoel
M
e
rge
bra
n
ch 'mast
e
r
'
of git
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-05-16
D
a
v
id van der Sp
o
el
Fixed scatt
e
r
in
g
function co
d
e in
g
_rdf
.
A
n
ew file
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Dav
i
d van de
r
Spo
e
l
Added mul
t
i
regre
s
s
ion analysis to g_analyze
.
See
info
.
.
.
commit
|
commitdiff
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tree
2010-05-16
David van der Spoel
Fixe
d
c
o
mpilation issue
in g
e
m
i
nate
.
c due
t
o n
o
n-defined
.
.
.
commit
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2010-05-16
David va
n
der Spoe
l
Merge br
a
n
ch 'master' of g
i
t@git
.
gromacs
.
o
rg:
g
romacs
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2010-05-12
D
a
vid van der Spoel
Merge branch 'ma
s
ter' of git
.
g
r
omacs
.
org:gromacs
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2010-05-12
David van
d
er Spoel
Delted two more superfluous f
i
les
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2010-05-11
D
av
i
d van der Spoe
l
Cleaned
u
p in top directory
.
Mov
e
d a few old
itp files
.
.
.
commit
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2010-05-11
Davi
d
v
a
n der Spo
e
l
Move
d
ph
o
sphate files int
o
gmx
.
f
f
directory
.
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