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Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4...
2011-04-04
David van der Spoel
M
erge branch
'
r
el
e
ase-4-5-
p
atches'
of git
@
git
.
grom
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
van
d
er Spoel
Removed
s
uper
f
luous file
.
commit
|
commitdiff
|
tree
2011-04-04
David
v
an d
e
r
Spoel
Made new programs comp
i
l
e
w
ith gcc
-pedan
t
ic
.
commit
|
commitdiff
|
tree
2011-04-04
D
a
vi
d
va
n
der Spoel
New entry
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
Added 1 an
a
l
y
sis tool ma
n
ual
.
commit
|
commitdiff
|
tree
2011-04-04
David van
d
er Spoel
Mer
g
e branch 'rel
e
a
s
e-4-5-patches'
i
nto orderpa
r
m
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n der Spoel
Latest fix
e
s from Bjorn S
t
een Saethre
commit
|
commitdiff
|
tree
2011-03-24
David van der
Spoel
Added Bjorn
'
s code, implemented running average filtering
.
commit
|
commitdiff
|
tree
2011-03-05
David van
d
er Spoel
M
erge branch 'release-4-5
-
patc
h
e
s
'
o
f git@gi
t
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David van der Spoel
Fixed SEGV in enec
o
nv
wh
e
n usin
g
the -e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David va
n
der Spo
e
l
Fixed mor
e
PBC an
d
i
n
dexing stuff
.
commit
|
commitdiff
|
tree
2011-01-30
Dav
i
d v
a
n der Spoel
Fixed
typo
.
commit
|
commitdiff
|
tree
2011-01-30
David van der
S
poel
Merge branch 're
l
ease-4-5-patches' into orderparm
commit
|
commitdiff
|
tree
2011-01-29
David
v
an de
r
Sp
o
el
Merge b
r
anch 're
l
e
ase-4
-
5-pa
t
ch
e
s' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
Da
v
i
d van der Spoel
Added code in g_nmei
g
to compute the qua
n
t
u
m cor
r
e
ctions
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David
van
der Spoel
Merge branch 'release-4-5-
p
atche
s
'
o
f gi
t
@git
.
grom
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van der Spoel
F
i
xed bug 67
8
w
h
i
c
h was due to c
a
lling gmx_fatal wi
t
hout
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
Dav
i
d van der Spoel
M
erge b
r
anch 'rel
e
ase-4-5-pat
c
h
e
s'
o
f git@git
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David va
n
d
er
S
poel
A
d
ded warning in g_dipol
e
s
commit
|
commitdiff
|
tree
2010-12-23
David van
der Spoel
Fixe
d
b
ug in s
t
atistics
which did
n
o
t allow
f
i
tti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David van d
e
r
S
poel
Merge branch 'rele
a
se-4-5-p
a
tches' of
git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Dav
i
d van der Spoe
l
Added 1
q
uote
.
commit
|
commitdiff
|
tree
2010-12-09
D
a
v
i
d van d
e
r Spoel
A
d
ded fata
l
error f
o
r
when
p
eople use energy
files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
David van
d
er Spoel
Fixed bug
z
ill
a
616 about formatting in the help
t
ext
.
commit
|
commitdiff
|
tree
2010-11-26
David van der Spoel
F
i
x
ed SEGV bug in g_sham
.
commit
|
commitdiff
|
tree
2010-11-18
David van der Spoel
M
a
d
e
pri
n
t
ing in check_multi_init conditional, d
e
pe
n
ding
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
D
a
vid van der Spoel
Fixed bug 608 by thr
o
win
g
a
fatal error in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
David van d
e
r Spo
e
l
M
e
r
ge branch 're
l
ease-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
D
av
i
d van der
S
poel
Merge
br
a
nch
'
release
-
4
-5-pa
t
ches' of git
.
gro
m
a
cs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
D
a
vid
van
d
e
r S
p
oel
Fixed compilation issu
e
s
wi
t
h C99 compa
t
i
bil
i
ty
.
commit
|
commitdiff
|
tree
2010-10-07
David va
n
der
S
p
oel
F
i
x
es and sma
l
l addit
i
ons to g_wham, due to Jochen
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David
v
an der Spoel
Re-added
g_kinetics
to
s
rc/tools/Mak
e
file
.
am
commit
|
commitdiff
|
tree
2010-09-25
D
a
vid
van der Spoel
Added softwar
e
-related qu
o
te
commit
|
commitdiff
|
tree
2010-09-24
D
a
v
i
d van der Spoel
Upda
t
ed to reflect bug 557
.
commit
|
commitdiff
|
tree
2010-09-20
David van der Spoel
Me
r
ge br
a
nch 'r
e
lease-4-5
-
patches' of g
i
t
@
g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
David v
a
n
der Spo
e
l
Fixe
d
bu
g
http://bu
g
zilla
.
groma
c
s
.
org/s
h
ow_bug
.
c
gi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David v
a
n der Spoel
C
orr
e
cted name of one of the devel
o
pers listed i
n
header
.
commit
|
commitdiff
|
tree
2010-09-14
D
a
vid van der Spoel
Fixed bug
553 by checking whether an atom name
i
s lo
n
ger
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David
van d
e
r Spoel
Fixed demo
to work with new pd
b
2gmx th
a
t requires
tw
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Dav
i
d
v
a
n der Spoel
Made genr
e
s
t
r -constr to produce constra
i
nts of type
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David van
d
er Sp
o
el
Fixed
b
ug 417
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Sp
o
el
Fixes more misery in function skipst
r
, where
p
ointer
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David va
n
der
Spoel
Add
e
d
t
wo
missi
n
g in
c
lude
f
iles
.
Fixed h
o
rrible coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Davi
d
v
an der
Sp
o
el
Fixed reuse of v
a
r
iable a
s
temp variable before pri
n
ting
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David van de
r
Spoel
Fixed bu
g
487 according to provided
patch
.
commit
|
commitdiff
|
tree
2010-08-03
Davi
d
van d
e
r Spoel
Fixed do
c
umentation text ac
c
ording to bugzilla 48
6
commit
|
commitdiff
|
tree
2010-08-01
David van der S
p
o
e
l
Me
r
ge
branch
'
r
e
lease-4-5-
p
atches'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David
v
an der Spoel
M
o
v
e
d pdb2top
.
h f
r
o
m src/ker
n
el to include to
a
l
low
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van
d
e
r
Spoel
Renamed typenam
e
to my_ty
p
ename in index
.
c
s
ince
typename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David van de
r
Sp
o
el
Fixed
compilation i
s
sue correspond
i
ng to bug 468
commit
|
commitdiff
|
tree
2010-07-14
Da
v
id van der Spoel
Fixed bu
g
467 re
a
ltin
g
to p
d
b
2
g
m
x
output of the wate
r
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
Da
v
i
d van d
e
r Spoel
Added citation for
scatterin
g
factors
.
Us
e
d in g_rd
f
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
Dav
i
d
v
an der Spoel
Adde
d
more at
o
ms to the scattering factor dat
a
file
.
commit
|
commitdiff
|
tree
2010-07-14
David van der S
p
oel
F
i
xed bug 462
.
p
db2
g
mx should now produ
c
e the correct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
David va
n
d
e
r
Spoel
Fixed bug
4
66 by comm
e
nting out the
offendin
g
li
n
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
Da
v
id van der Spoel
Merge branch 'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-12
David va
n
der
S
poel
Added
ini
t
iali
z
a
t
ion o
f
pbc
st
r
uct
i
n
g
enb
o
rn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
David van
d
er Spoel
Added in
i
tia
l
ization
o
f pbc structu
r
e before
calc_gb
_
forces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David v
a
n
der Spoel
Merge branch 'mas
t
er' of gi
t
.
g
r
omacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-08
Davi
d
van
der Spoel
Added bondedtyp
e
s section to r
t
p files
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
Da
v
id van der Spoel
Re
m
oved pos
s
ible
SEGVs in rmpbc in case ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d
van der Sp
o
el
Merge branch '
m
aster' of g
i
t
.
gromacs
.
org
:
gr
o
ma
c
s
commit
|
commitdiff
|
tree
2010-07-07
David van der Spoel
Merge branch 'master' of git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Da
v
id
van der Spoel
F
i
xe
d
m
i
s
e
r
a
ble
b
u
g
in commrec
.
h where
a
n i
n
t array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David
van der Spoel
Fixed bug in gmx
_
sumf_com
m
wh
e
re
a double ar
r
ay w
a
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David va
n
der Spoe
l
Me
r
ge br
a
nch '
m
aster' o
f
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-05
David va
n
der Spoel
Merge bra
n
ch 'master' of
g
it
.
gromacs
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2010-07-05
D
a
vid v
a
n der
S
poel
Add
e
d sfactor
.
dat
to the i
n
stallation targe
t
s in
s
hare
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
D
a
v
i
d
van der
S
p
oel
Fixed inc
l
u
de stateme
n
ts such that
double
p
reci
s
ion
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David
v
an der Spoel
Merge branch '
m
aster
'
o
f
git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Made remov
i
ng p
b
c non-static
.
T
h
is affects ma
n
y analysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
D
av
i
d
v
a
n
der Spoel
Merge
br
a
n
ch 'master'
of gi
t
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-02
D
avid
v
a
n der
Spoel
Fix
e
d
bug http://bugzilla
.
g
r
omacs
.
org
/
show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Spo
e
l
Fixed h
t
tp://bugzilla
.
gr
o
macs
.
org/sh
o
w_
b
ug
.
cgi?id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Spoel
Me
r
ge
b
ranc
h
'
m
a
ster'
o
f git
.
g
romacs
.
o
r
g:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-30
David
v
a
n
de
r
Spoel
Fixed bug in b-fac
t
ors output
b
y g_confrms
.
T
he
y
were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van
d
er Spoel
A
d
d
ed missing ar
g
ument step
t
o tr
o
tter_update
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David va
n
der Spoel
Merge branch 'm
a
ster'
o
f git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
U
p
dated CMakeLists
.
txt i
n
ngmx dire
c
tory to exclud
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Sp
o
el
Fix
e
d
m
any issues
r
e
g
arding to
com
p
ilation w
i
th C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der Spoel
Fixed Makefi
l
e
.
am leading to
w
arnin
g
s
.
commit
|
commitdiff
|
tree
2010-06-14
Da
v
id van der Spoel
Fixed make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
Da
v
id
van der Spoel
Merge
b
ranch 'master' of git
.
gromacs
.
org:g
r
o
m
acs
commit
|
commitdiff
|
tree
2010-06-14
David
van der S
p
o
e
l
Ad
d
e
d
more fixe
s
i
n
comment
t
exts, generousl
y
provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
D
a
vid van der
S
p
oel
F
i
xed
a
lot of
spel
l
i
ng errors i
n
com
m
e
n
ts an
d
documentat
i
on
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David
van der Spoel
Merge bran
c
h 'mast
e
r
'
of gi
t
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David van
d
er Sp
o
e
l
Fixed
for
c
e fi
e
ld fil
e
s for ATP in order to cl
e
ar
b
ug
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Me
r
ge
branch 'master' of git
.
gromac
s
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Made lege
n
d mor
e
or less
work in g_chi
.
Don't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David v
a
n
der S
p
oel
Fixed SEGV in
g
_chi as des
c
ribed i
n
bug
4
30
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der
S
poe
l
A
dded option -n
o
pbc to g
_
rmsdis
t
in o
r
der to
fix
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
va
n
der
S
po
e
l
Pedantic chang
e
in
t
h
e check
w
hether a filen
a
me is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van der Spoel
Renam
e
d some
pro
g
rams to follow
t
he g_ doctrine: luc
k
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
C
l
ea
n
ed up and renamed f
i
l
es in ngmx directory to bett
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der Spoel
R
enamed
s
ome
files in a roundabout way
to ad
h
ere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
a
n
der Spoel
Removed
a
vera
g
e
.
c
,
that
fu
n
ctiona
l
ity is now in g_ana
l
yze
.
commit
|
commitdiff
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2010-06-10
David van
d
er S
p
oel
F
i
xed
s
t
r
a
nge
t
y
p
o in gm
x
_di
h
.
c
commit
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2010-06-06
Davi
d
van der Spoel
Mov
e
d w
a
rning message in add_atomtype t
o
be printed
.
.
.
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2010-06-03
David van der Spoel
Made x2top (very) slightl
y
function
a
l
a
ga
i
n
.
Still
.
.
.
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2010-06-02
Da
v
id van der Spoel
C
h
anged erro
r
message fo
r
settle p
r
oblems, such that
.
.
.
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