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Merge branch 'release-4-5-patches'
2010-08-03
David van der
S
poel
Me
r
ge branch
'
release-4-5
-
patch
e
s
'
commit
|
commitdiff
|
tree
2010-08-03
D
avi
d
van
der Spoel
Fi
x
ed docu
m
e
n
ta
t
ion text ac
c
ording to bugzill
a
486
commit
|
commitdiff
|
tree
2010-08-01
Da
v
id van der Spoel
Merg
e
branch 'release-4
-
5-patches' of g
i
t
.
g
r
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Da
v
id van
d
er Spo
e
l
Moved pdb2top
.
h from src/ker
n
el to
incl
u
de to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
D
avi
d
v
a
n der Spoel
R
e
name
d
ty
p
e
name to
my_typename in i
n
dex
.
c
since typenam
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
D
a
vid van d
e
r
Sp
o
el
Fixed
co
m
pilation issue
corres
p
onding to
bug 468
commit
|
commitdiff
|
tree
2010-07-14
Dav
i
d
van
d
er S
p
oel
Fixed bug 467 r
e
altin
g
to pd
b
2
g
mx
output of the water
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der
Sp
o
el
A
d
d
e
d
citation for scattering factors
.
Used in g_rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
D
avid v
a
n der
S
poel
Added
more
atoms to the s
c
attering factor d
a
t
a f
i
le
.
commit
|
commitdiff
|
tree
2010-07-14
D
a
vid va
n
der Spoel
Fixed bug 4
6
2
.
pdb2g
m
x should now
produ
c
e
the correct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
David van
d
er Spoel
Fixed bug 4
6
6 b
y
co
m
me
n
t
ing out
the offendin
g
lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David van der
S
poel
Merge branch
'maste
r
'
of g
i
t@g
i
t
.
gromacs
.
org:gro
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-12
David van der Spoel
Added
i
nitial
i
zation
of pbc stru
c
t in gen
b
orn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
Da
v
id
v
an de
r
Spoel
Added ini
t
iali
z
a
t
ion o
f
pb
c
structure before calc_gb_
f
orce
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
D
avi
d
van
d
er S
p
oel
Merge br
a
n
ch
'
maste
r
' of
g
it
.
g
r
o
ma
c
s
.
o
r
g:groma
c
s
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d van der Spoel
Added
bondedtypes section t
o
rtp fi
l
es
.
It mi
g
ht be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
D
a
vid v
a
n der Spoel
Rem
o
ved
p
ossible SEG
V
s in rmpbc in case ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
Spoel
Merge branch 'master
'
of git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-07-07
David van der Spo
e
l
Mer
g
e
branch 'master'
o
f
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-07
David van der Spoel
Fixed misera
b
le bug in commrec
.
h wher
e
an
int array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Da
v
id
v
an d
e
r Spoel
Fixed b
u
g
in gm
x
_sum
f
_comm where a doubl
e
a
r
r
ay was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Davi
d
va
n
der Spoel
M
e
rge branc
h
'
m
aster'
of
g
it
.
gromacs
.
org
:
groma
c
s
commit
|
commitdiff
|
tree
2010-07-05
David v
a
n
d
e
r
S
poe
l
Merge branch 'master' of git
.
gromac
s
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2010-07-05
D
a
v
i
d van der
Spoe
l
Adde
d
sfa
c
tor
.
dat
t
o
the
installation targets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
David van der Spoel
Fixed
include statements
suc
h
that doubl
e
precision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
D
a
v
id van der Spoel
Me
r
ge bra
n
ch 'm
a
ste
r
' of
g
it
.
groma
c
s
.
o
r
g:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-02
Da
v
id
van d
e
r
S
poel
Made rem
o
ving pbc non-
s
tatic
.
This affect
s
many analysi
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David
v
a
n
der Spoel
Merge branch 'm
a
s
ter' of git
.
gromacs
.
or
g
:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Fixed bug http
:
//bug
z
illa
.
gromacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van
de
r
Spoel
Fixed http://bugzilla
.
gromacs
.
org/sh
o
w_bug
.
cgi?id
=
457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
D
avid van der Spoel
M
e
r
ge branch 'master'
o
f git
.
g
romacs
.
o
r
g:grom
a
c
s
commit
|
commitdiff
|
tree
2010-06-30
D
avid van der Sp
o
el
Fixe
d
b
u
g
in b-fa
c
tors out
p
ut by
g
_
confrms
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
Added
missing argumen
t
step to trot
t
er_update
.
H
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
van d
e
r Spo
e
l
Merge bra
n
ch 'master
'
of
g
i
t
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-27
Da
v
i
d
van der Spoel
Upd
a
te
d
CMakeLists
.
t
xt
in
ngmx
d
irectory to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van de
r
Spo
e
l
F
i
xed ma
n
y
i
ssues regar
d
in
g
to compi
l
a
tion with C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der S
p
o
e
l
Fixed Makefil
e
.
am le
a
ding to
warni
n
gs
.
commit
|
commitdiff
|
tree
2010-06-14
D
a
vid van der S
p
oel
F
ixed make_e
d
i
.
c
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Merge branch 'master' of git
.
grom
a
cs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-14
D
a
vid van de
r
Spoel
Added more fixes in comment texts, generously provide
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
D
avid van der Spoel
Fixed a lot of s
p
elling
e
rrors in c
o
mme
n
ts
a
n
d documentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
M
erge branch 'm
a
ster
'
of
g
it
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-06-11
D
a
v
id v
a
n der Sp
o
e
l
Fi
x
ed for
c
e
field files
fo
r
ATP in o
r
der to clear bug
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Merge
b
ran
c
h
'
m
aster' of
git
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
id van der Spoel
Made legend m
o
re or less work in g_chi
.
Don'
t
know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der Spoel
Fixed SEGV
i
n g_chi a
s
described in bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid v
a
n
der
S
poel
A
dded option -nopbc to g_rmsdist
in order to
f
ix
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
v
a
n der S
p
oel
Pedantic
c
ha
n
ge in the check
w
hether a filename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
der S
p
oel
Renamed some programs to fo
l
low the g_ do
c
trine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van der S
p
oel
C
l
eaned up an
d
renamed
f
i
les i
n
ngmx directory to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der
S
poe
l
Renamed some files
in a roundabo
u
t w
a
y
t
o adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
id van
d
e
r Spoe
l
R
em
o
ved ave
r
a
ge
.
c, that functiona
l
i
ty is now in g_a
n
alyze
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van d
e
r Spoel
Fixed s
t
range
typo
i
n gmx_d
i
h
.
c
commit
|
commitdiff
|
tree
2010-06-06
David v
a
n d
e
r Spoel
Moved warning message
in add_atomtype to
b
e printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David van der Spoel
Made x2to
p
(very
)
s
li
g
htly functional again
.
S
till
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d
v
a
n der
Spoel
Change
d
error message for settle p
r
oblems, such that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
A
d
ded
e
x
plicit
ang
l
e
in
ACE
dec
l
aration in
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Sp
o
el
F
i
xed type
in gmx_morph
.
c:
e
fT
R
O ->
efT
R
X
wh
i
ch lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van d
e
r
S
p
o
el
F
i
xed
bug
3
96
.
In
f
a
ct it was alrea
d
y fixed partly
.
commit
|
commitdiff
|
tree
2010-06-02
David va
n
der Spoel
Fixed bu
g
4
0
1 by implementi
n
g the proposed patch that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid van
d
er Spoel
Fixed bug
3
81 by adding the number of the first atom
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
avi
d
van der Spoel
Fixed b
u
g 349
.
The f
i
le m
a
d
e
with the
-vis option has
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
avid van der Sp
o
el
Merge b
r
anch 'master' o
f
g
it
.
grom
a
c
s
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-02
David
v
an d
e
r Spoel
Rem
o
ved option CAN_DT
from g_msd, s
i
nce
i
t
c
anno
t
handl
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David v
a
n
d
er Sp
o
el
Increased buffer s
i
ze for
reading in
a
whole file at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
David
van der S
p
o
e
l
Merge branch 'master'
o
f git
.
gr
o
m
a
cs
.
org
:
g
r
o
macs
commit
|
commitdiff
|
tree
2010-05-25
David van d
e
r
Spoel
Added one more!
commit
|
commitdiff
|
tree
2010-05-24
Davi
d
v
an der Sp
o
el
Removed
C++ style comments
in mdrun
.
commit
|
commitdiff
|
tree
2010-05-21
David van der Spoel
Fixed c
o
mpilation warnings and
removed spurious C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
David
van der Spoel
Added 1
commit
|
commitdiff
|
tree
2010-05-20
David van der Spoel
Made
g
_a
n
a
l
yze
compile aga
i
n, but ot link yet
.
commit
|
commitdiff
|
tree
2010-05-19
D
a
vid van d
e
r Spoel
Merge branch
'master' of git
.
gromac
s
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-05-19
D
avid van der Spoe
l
Adde
d
c
heck in
r
ead_
p
d
b
for e
x
ist
e
n
c
e of t_re
s
in
f
o
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
D
a
vi
d
van
d
e
r Spoel
A
d
ded a cool
q
uote,
an
d
r
e
m
ov
e
d
t
wo c
o
mma's in openmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Dav
i
d v
a
n der Spoel
Me
r
ge branch 'm
a
ster
'
of
g
it
.
grom
a
cs
.
o
rg:gromac
s
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
Fixed scattering function code in g_
r
df
.
A new fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
A
d
ded m
u
lti regre
s
sion analysis to g_an
a
lyze
.
See in
f
o
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
D
a
v
id van der Spoel
Fi
x
ed compilation issue in geminate
.
c due to non-defined
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van
d
er S
p
o
e
l
Merg
e
branch 'ma
s
ter'
of git@git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
Dav
i
d van d
e
r
S
poel
Merge
b
ran
c
h 'master'
o
f git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-05-12
Dav
i
d van
d
er
Spoel
Del
t
e
d
t
wo more superfluous fi
l
es
commit
|
commitdiff
|
tree
2010-05-11
D
a
vid van der Spoel
Clea
n
e
d
u
p
in top director
y
.
Move
d
a
few
o
ld itp files
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
David van d
e
r
Spoel
Move
d
phosph
a
te
f
iles into gmx
.
ff di
r
ector
y
.
commit
|
commitdiff
|
tree
2010-05-11
D
a
vi
d
van der Spoel
Moved prop
a
nol itp f
i
le t
o
p oplsaa
.
ff, removed two
.
.
.
commit
|
commitdiff
|
tree
2010-05-02
David va
n
der
S
poe
l
Mer
g
e bran
c
h 'm
a
ste
r
' of
g
it@
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-04-30
David van der Spoe
l
Added one
commit
|
commitdiff
|
tree
2010-04-26
David v
a
n
der Sp
o
e
l
Made hist
o
gramming slightly more flexible
.
Used
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-04-12
David va
n
der Spoel
Merge bra
n
ch 'master'
of gi
t
@git
.
groma
c
s
.
org
:
gromac
s
commit
|
commitdiff
|
tree
2010-04-12
David van der Spoel
Cha
n
ge
d
th
e
output of topology fil
e
s to inclu
d
e the
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
David van de
r
Sp
o
el
Merge branch 'mas
t
er' o
f
git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-04-06
Dav
i
d van der Spoel
A
d
d
ed statement t
o
set
r
t
p
t
o
NULL
.
commit
|
commitdiff
|
tree
2010-04-06
David van der Spoel
R
ev
e
rt "Added arg
u
m
e
nt rtpname to t_ato
m
s
_
set_res
i
nfo
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
D
a
v
id
van der S
p
oel
Added argument rtpname to t_atoms_se
t
_
resinfo to avo
i
d
.
.
.
commit
|
commitdiff
|
tree
2010-04-04
D
avid van der
S
poel
Ad
d
ed
o
ne
.
commit
|
commitdiff
|
tree
2010-04-04
Davi
d
va
n
d
er Spoel
M
erge
b
ranch 'master' of git
.
groma
c
s
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-03-31
Da
v
id van d
e
r Spoel
Added on
e
commit
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commitdiff
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tree
2010-03-12
D
avid van der Spoel
Merge
branch 'master' of git
.
gromac
s
.
org:
g
ro
m
acs
commit
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commitdiff
|
tree
2010-03-12
David v
a
n der Spoel
A
d
ded flush af
t
er wr
i
ting to debug file
commit
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commitdiff
|
tree
2010-03-11
David van d
e
r Spoel
Aded function copy
_
t
_
a
toms, u
p
dated functi
o
n add_t_atoms
.
.
.
commit
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commitdiff
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tree
2010-03-10
D
av
i
d van der Spoel
Merge branc
h
'ma
s
ter' of git@
g
it
.
g
r
omacs
.
org:g
r
omacs
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