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A freeze group can now be allowed to move rigidly in some dimension by using "freezed...
2011-04-10
David van der Spoel
Merge bran
c
h 'release-4-5-
p
atch
e
s' of
g
i
t
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
Da
v
id van der Spoel
Added g_hyd
o
rder
.
1 man page
.
commit
|
commitdiff
|
tree
2011-04-06
David van der
S
poel
Fixed
header for gmx_conect_
i
nit
commit
|
commitdiff
|
tree
2011-04-04
David van d
e
r Spoel
M
e
rge
b
r
anch '
r
elease-4-
5
-patches' of git@git
.
g
rom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
David van der
S
poel
Re
m
ove
d
s
u
perfluous file
.
commit
|
commitdiff
|
tree
2011-04-04
D
a
vid
v
an der Sp
o
el
Made new programs co
m
p
ile
w
i
th gcc -pedantic
.
commit
|
commitdiff
|
tree
2011-04-04
David van der S
p
oel
New entry
commit
|
commitdiff
|
tree
2011-04-04
D
av
i
d van der Spoel
Added 1 analysis tool m
a
nual
.
commit
|
commitdiff
|
tree
2011-04-04
Dav
i
d van der Spoel
Merge branch 'rele
a
se-4-5-pat
c
hes' i
n
t
o
orderparm
commit
|
commitdiff
|
tree
2011-04-04
David va
n
d
e
r Spoel
Latest fixes from Bjorn Steen Saethre
commit
|
commitdiff
|
tree
2011-03-24
Dav
i
d
van
d
e
r
S
poel
Adde
d
Bjorn's
code, implemented running
a
verage filt
e
ring
.
commit
|
commitdiff
|
tree
2011-03-05
Dav
i
d va
n
der S
p
oel
Merg
e
branch 'r
e
lease-
4
-
5
-
patches' o
f
git
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
Davi
d
van de
r
Spoel
F
ixe
d
SEGV in eneconv when using th
e
-e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Sp
o
el
Fixed mor
e
PBC and indexing stuff
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
van der
S
poel
Fixed typ
o
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
van
der
Spoel
Merg
e
b
ranch 'release-4-5-patches' i
n
to orderpar
m
commit
|
commitdiff
|
tree
2011-01-29
David van der Spoel
Merge branch 'rele
a
se-4-5-
p
atches'
of git@git
.
gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
Dav
i
d
v
an der Spoel
Added code i
n
g_nmeig to compute
the qua
n
tum correct
i
ons
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
D
avid v
a
n der Spoel
Merge
bra
n
ch 'r
e
l
e
ase-4-5-patches' of git@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van der
S
poel
F
ixed
b
ug 678 which was due to calling gm
x
_f
a
tal w
i
thout
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
Da
v
id van d
e
r Spoel
Mer
g
e bra
n
c
h 'release-4-5-patches' of
g
it@
g
it
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
D
avid van der Spoel
Added war
n
ing i
n
g_dipoles
commit
|
commitdiff
|
tree
2010-12-23
David va
n
d
er Spoel
Fix
e
d
b
ug
i
n
statist
i
cs which
did n
o
t allow
f
i
tting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
a
vid v
a
n
der
S
p
o
el
Merge branch 'release-4
-
5-p
a
tc
h
es' of git
.
gromac
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David van der S
p
o
el
A
d
ded 1
q
uote
.
commit
|
commitdiff
|
tree
2010-12-09
David
v
a
n der Spoel
Added fatal error for when
people use energy f
i
l
es
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
D
a
vid van d
e
r
Spoel
Fi
x
ed bugzilla 616 a
b
o
u
t
f
ormatting in
the help text
.
commit
|
commitdiff
|
tree
2010-11-26
D
avid van
d
er
Spoel
Fi
x
ed
S
EG
V
bug
i
n
g
_
s
ham
.
commit
|
commitdiff
|
tree
2010-11-18
David
va
n
der Spoel
Made printing in
c
heck
_
m
u
lti_init
conditional, depending
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Dav
i
d v
a
n der S
p
oel
Fix
e
d bug 608
by
throwing a fa
t
a
l
error in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
David van de
r
Spoel
Merge bran
c
h 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
Da
v
id v
a
n
d
e
r Spoel
Merg
e
branch 'rel
e
a
se-4-5-p
a
tches' of git
.
gro
m
acs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
D
avi
d
van d
e
r
Spoel
Fixed compilation i
s
sues with C99
compati
b
ility
.
commit
|
commitdiff
|
tree
2010-10-07
David van der Spo
e
l
Fi
x
es
and
small addi
t
ions to g_wh
a
m, due to
J
o
chen
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
D
a
vid va
n
der Sp
o
el
Re-added g_kinetics
t
o
s
rc/
t
ools/
M
a
kefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
David va
n
der Spoel
A
d
ded software-rela
t
ed quote
commit
|
commitdiff
|
tree
2010-09-24
David van der Sp
o
el
Upd
a
ted to
reflect bu
g
5
57
.
commit
|
commitdiff
|
tree
2010-09-20
D
a
vid
van
d
er
S
poel
Merge branc
h
'
r
elease-
4
-5-patches' of git@git
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
David van de
r
Spoel
Fixed bug http://bu
g
z
i
lla
.
gr
o
m
a
cs
.
or
g
/
s
ho
w
_
b
ug
.
c
g
i
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
D
avid van der Spo
e
l
Correc
t
ed name
o
f
one of the developer
s
l
i
sted in header
.
commit
|
commitdiff
|
tree
2010-09-14
David van
d
e
r
Sp
o
el
Fixed bug 553 b
y
ch
e
cking whether an atom name is longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
Dav
i
d
v
an
d
er Spoel
Fixe
d
demo to work with
new
p
db
2
gmx
t
h
a
t requires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David
v
a
n der Spoel
Mad
e
genrestr -constr to
p
roduce constraints
o
f
t
yp
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David v
a
n
der Spoel
F
i
xed
bug
4
17
.
commit
|
commitdiff
|
tree
2010-08-19
David v
a
n der Spoel
Fixes mo
r
e mi
s
ery in func
t
io
n
skipstr, wh
e
re poin
t
er
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David v
a
n
der Spoel
Added two missing incl
u
de files
.
Fixed
horrible co
d
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
D
a
vid van der S
p
oel
Fixed reuse
o
f variable as te
m
p varia
b
l
e
b
efore
p
rinting
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David v
a
n
der Spo
e
l
Fixed
b
ug 4
8
7 according
t
o provided patch
.
commit
|
commitdiff
|
tree
2010-08-03
D
a
vid
v
a
n der Spoel
F
ixed document
a
ti
o
n
text according
t
o bug
z
illa
4
86
commit
|
commitdiff
|
tree
2010-08-01
David van der S
p
oe
l
Mer
g
e branch 'release-4
-
5
-
patc
h
e
s
'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David van der Spo
e
l
Moved pdb2top
.
h from s
r
c
/
ker
n
el to include
t
o al
l
ow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van
d
e
r
Spoe
l
Re
n
amed typen
a
me to my
_
type
n
a
m
e in in
d
ex
.
c sin
c
e type
n
ame
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David van der S
p
oel
Fixed
compil
a
tion
issue corresponding to
b
ug 4
6
8
commit
|
commitdiff
|
tree
2010-07-14
David
v
an
d
er Spoel
F
ixed bug 4
6
7 realti
n
g to pdb2gmx
o
u
t
p
u
t
of the water
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
A
d
de
d
ci
t
ation
for scatterin
g
f
a
c
t
ors
.
U
s
e
d
in
g
_
rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David v
a
n der Spoel
A
dd
e
d more atoms to the scat
t
er
i
n
g
factor d
a
ta file
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
F
i
xed
b
ug 462
.
pdb2gm
x
should
now produce the corre
c
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
Da
v
id
van der S
p
oel
Fixed bug 466 by
c
ommenting
o
u
t
the offen
d
ing l
i
nes
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d
v
a
n
der Spoel
Merge
b
r
anch '
m
ast
e
r' of g
i
t@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d van
der Spoel
Added initiali
z
ation o
f
pbc struct in genbor
n
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
Davi
d
van der Sp
o
el
Adde
d
initia
l
i
zation of p
b
c
struct
u
re before calc_gb_
f
orce
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der Spoe
l
M
erge br
a
nch 'mas
t
e
r
'
o
f
git
.
gromacs
.
o
rg:gromac
s
commit
|
commitdiff
|
tree
2010-07-08
David v
a
n der Spoel
A
d
ded bond
e
dtype
s
sec
t
ion t
o
rtp files
.
I
t
migh
t
be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
S
p
oel
Removed possibl
e
SEGVs in
rmpbc in case
e
PBC = N
o
.
commit
|
commitdiff
|
tree
2010-07-08
David van der Spoel
Merge branch
'
master
'
o
f
git
.
gro
m
acs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-07
Davi
d
va
n
de
r
Spoel
Mer
g
e branch 'ma
s
ter'
o
f
git
.
g
r
o
macs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-07
David van der
S
poel
Fixe
d
m
iserable bu
g
in commrec
.
h
w
here
an
i
nt array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David van der Sp
o
e
l
Fixe
d
bug in gmx_sumf_comm where a doub
l
e a
r
r
ay
w
as
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David van der Spo
e
l
Merge branch
'mas
t
e
r' of git
.
gro
m
acs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-05
Dav
i
d van
d
er Spoel
Merg
e
branc
h
'master' of git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-05
David van der Spoel
Added sfactor
.
dat to th
e
installation targets in
sha
r
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
Dav
i
d van der Spoel
Fixe
d
inc
l
u
d
e stat
e
ments su
c
h
tha
t
double
p
recisio
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Merge
b
r
anch 'master' of git
.
gr
o
macs
.
or
g
:g
r
om
a
cs
commit
|
commitdiff
|
tree
2010-07-02
David va
n
der Spoe
l
Made
r
emov
i
ng pbc
non-static
.
This af
f
ects m
a
n
y
a
nalysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David
van der
Spoe
l
Merge br
a
nch 'mas
t
er'
o
f git
.
gr
o
macs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
F
i
xed bug h
t
t
p
://bugzill
a
.
gro
m
acs
.
org
/
sh
o
w
_
bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
D
a
vid v
a
n der Spoel
Fixed htt
p
://bugzilla
.
gromacs
.
org/show_bug
.
cgi
?
id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
D
avid van der
Spoel
Mer
g
e branch 'mas
t
er' of gi
t
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-30
David van de
r
Spoel
F
ixe
d
bu
g
in b-fact
o
rs output by
g
_
c
onfr
m
s
.
Th
e
y were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Dav
i
d
van der S
p
oel
A
dded mis
s
ing argument
s
tep to t
r
o
t
ter_update
.
H
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Davi
d
va
n
der Spoel
Merge
b
ranch 'ma
s
te
r
'
of g
i
t
.
gromacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-27
Davi
d
van der S
p
oel
Updated CMakeLists
.
txt in
n
gmx
directory to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
Fixed many
issues regarding to
c
ompilation
w
i
t
h C
+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
D
avid van
d
er Spoel
Fi
x
ed Makefile
.
am le
a
ding to wa
r
n
i
ng
s
.
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Fixed make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
David van der
Spoel
M
erge branch 'master'
o
f git
.
grom
a
cs
.
org:gr
o
mac
s
commit
|
commitdiff
|
tree
2010-06-14
David va
n
de
r
S
poe
l
Added more f
i
xes i
n
comm
e
nt texts, generousl
y
provid
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Dav
i
d van der S
p
o
e
l
F
i
xed
a
lot of spel
l
ing e
r
rors
i
n
c
o
mment
s
and documentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David
van der Spoel
Merge branc
h
'm
a
ster' of git
.
gromacs
.
org
:
gromac
s
commit
|
commitdiff
|
tree
2010-06-11
Da
v
id
van der
Spoel
F
ixed force field file
s
for
A
TP in
order
to clear bug
commit
|
commitdiff
|
tree
2010-06-10
David van der
S
poel
Merge branch 'master' o
f
git
.
groma
c
s
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d van der Spoel
Made l
e
gend more or
l
e
ss work in
g
_
c
hi
.
D
o
n't
know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David v
a
n der Spoel
Fixed SE
G
V
i
n
g_chi
a
s describe
d
i
n
bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der
S
poe
l
Added option -nopbc to g_rmsdist
in o
r
de
r
to fix
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van der Spoe
l
Pedant
i
c
chang
e
i
n
t
h
e check whether a
fi
l
ename i
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
d
er S
p
oel
R
enamed s
o
me program
s
to
f
ol
l
ow the g
_
d
o
ctrine
:
luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van d
e
r Spoel
Cl
e
a
n
e
d up an
d
renam
e
d files in ngmx direc
t
ory to
better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Da
v
id van d
e
r Spoel
Renamed some
fil
e
s i
n
a
roun
d
a
b
out way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der Spoel
Removed average
.
c, that func
t
ionality is
n
o
w
in g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
Da
v
id van der Spoel
F
i
x
ed strange typo i
n
gmx_dih
.
c
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|
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