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Added 1 analysis tool manual.
2011-04-04
Davi
d
v
an
d
e
r
S
p
oel
A
dd
e
d 1 analysis
t
o
o
l
ma
n
ual
.
commit
|
commitdiff
|
tree
2011-04-04
D
avid van d
e
r
Spo
e
l
Merge
b
ranch
'release-4-5-patches' into orderparm
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
L
ates
t
f
ixe
s
from
Bjo
r
n Steen Saethre
commit
|
commitdiff
|
tree
2011-03-24
David van d
e
r Spoe
l
Added Bjorn's code,
i
mplemente
d
r
unning a
v
erage filte
r
i
ng
.
commit
|
commitdiff
|
tree
2011-03-05
Davi
d
van
d
er Spoel
Merge
branch 'relea
s
e
-4
-
5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
Da
v
i
d van der
S
poel
Fixed SEGV in eneconv when using
the -e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
F
ixed more
P
BC and inde
x
ing stuff
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
v
an
d
e
r Spo
e
l
Fixed typo
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
M
er
g
e bran
c
h 'releas
e
-4
-
5
-
pa
t
ches' into
o
rderpa
r
m
commit
|
commitdiff
|
tree
2011-01-29
Da
v
id van der
Spoel
Merge
b
ranch 'release-4
-
5-
p
at
c
hes' o
f
git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
Davi
d
va
n
der
S
poel
A
d
ded code i
n
g_nme
i
g to comp
u
te t
h
e quantum
c
orre
c
tions
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David van der Spoel
Mer
g
e branch '
r
elease-4-5-
p
atches' of git@git
.
g
r
o
m
acs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
Da
v
id van d
e
r
Spoel
Fixed bug 678 which w
a
s due to c
a
ll
i
ng gmx_fat
a
l withou
t
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
David van de
r
Spoel
Me
r
ge
b
r
anch 'rele
a
se-4
-
5-patches' of git@gi
t
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
Dav
i
d van d
e
r
S
poe
l
Ad
d
e
d warn
i
ng in g_dipoles
commit
|
commitdiff
|
tree
2010-12-23
David van de
r
Spoel
Fi
x
e
d
bug in stati
s
tic
s
which did not
all
o
w fitt
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
avid van der Spoel
M
e
rg
e
branch 'r
e
le
a
se-4-5-patche
s
' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Da
v
id
v
an
d
er Spo
e
l
Added 1 quote
.
commit
|
commitdiff
|
tree
2010-12-09
Da
v
id van
der Spoel
Added fat
a
l
e
r
ror for when
p
eople use
e
nergy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
David van der Spoel
F
i
x
e
d bu
g
z
i
lla 616 abo
u
t formatting i
n
the he
l
p
text
.
commit
|
commitdiff
|
tree
2010-11-26
David van de
r
Spoel
F
ixed SEGV
b
u
g in g
_
sham
.
commit
|
commitdiff
|
tree
2010-11-18
David van der Spoel
Made printing i
n
check_mul
t
i_init condition
a
l, depending
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Da
v
id van der S
p
oel
F
ixed b
u
g 608 by throwing a fa
t
al e
r
ror in
g
rom
p
p
.
commit
|
commitdiff
|
tree
2010-10-28
David van der Sp
o
el
Merge bra
n
ch 'release-4-
5
-patch
e
s' o
f
gi
t
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David van de
r
Spoel
Merge
b
ranch 'release-4-5-
p
a
t
ches' of
g
it
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David van der Spoel
Fixed
c
ompilation issues
w
ith C99 compatibi
l
ity
.
commit
|
commitdiff
|
tree
2010-10-07
David
v
an der Spoel
Fixes and small
additions t
o
g_wham, due to
J
oche
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
Da
v
id
v
an d
e
r
Spoel
Re-added g_kinetics to s
r
c/tools/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
Da
v
id van der Spoel
Added
softwar
e
-related quote
commit
|
commitdiff
|
tree
2010-09-24
David
van der Spoe
l
U
p
dated to ref
l
ect bug 55
7
.
commit
|
commitdiff
|
tree
2010-09-20
David van
der Sp
o
el
M
e
r
ge branch 're
l
e
a
se-4-5-patches' of git@g
i
t
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Da
v
id van der
S
poel
Fix
e
d bug http
:
//bugzilla
.
gromacs
.
o
rg
/
s
how
_
bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David
v
a
n der Spoel
Correct
e
d
name of one of the developers list
e
d
i
n
h
eader
.
commit
|
commitdiff
|
tree
2010-09-14
D
a
vid van der Spoel
F
ixed
bug 5
5
3 by chec
k
ing whether an atom nam
e
is longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
D
a
vid va
n
de
r
Spoe
l
Fixed demo
t
o
w
ork with
n
ew p
d
b2gmx t
h
at requires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
D
a
v
i
d
van der Spoel
Made genrestr -
c
on
s
tr to produce const
r
aints of
t
y
p
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
D
a
v
id van der S
p
oe
l
F
i
xed bug 4
1
7
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Fixes mor
e
m
i
sery in
f
unction s
k
ipstr, where p
o
int
e
r
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Added two missing in
c
l
ude file
s
.
Fixed
hor
r
ible coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David
van
d
er
S
poel
Fixed reus
e
of varia
b
le as temp variab
l
e be
f
ore prin
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
D
a
vid van
d
er Spoel
Fixe
d
bug 4
8
7 accordi
n
g
to provided patch
.
commit
|
commitdiff
|
tree
2010-08-03
David
v
an
d
er Spoel
Fix
e
d documentation
t
e
x
t
a
c
cord
i
ng to bu
g
zi
l
la 4
8
6
commit
|
commitdiff
|
tree
2010-08-01
David van der Sp
o
el
M
erge branch 'rel
e
a
s
e-4-5-pat
c
h
e
s' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David va
n
der Spoel
Moved pdb2top
.
h from src/kernel to include t
o
allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
Davi
d
van der Spoel
Renam
e
d t
y
penam
e
to my_ty
p
en
a
m
e
i
n ind
e
x
.
c sin
c
e typename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
D
avi
d
van der Spo
e
l
Fixed compilatio
n
issue corresponding
t
o bug 468
commit
|
commitdiff
|
tree
2010-07-14
Davi
d
van der Spoe
l
Fix
e
d bug 467
r
ealting to pdb2gmx output o
f
the wat
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
D
avid van der
Spoel
Added citation for
s
catteri
n
g factors
.
U
s
ed
i
n g_rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van d
e
r Spoel
A
dded m
o
r
e atoms
to the scattering fa
c
t
o
r data file
.
commit
|
commitdiff
|
tree
2010-07-14
Da
v
id v
a
n d
e
r Spo
e
l
F
i
x
e
d bu
g
462
.
p
d
b2gmx shoul
d
n
o
w produce t
h
e correct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
D
avid
v
an der Spoel
Fixed bug
4
66
b
y co
m
me
n
ting out the offending lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David
v
an der
S
po
e
l
M
e
rg
e
branch 'm
a
ster' of git@gi
t
.
gro
m
a
c
s
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-12
David va
n
der Spoel
Added
initialization of pbc
struct in gen
b
orn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
Davi
d
van der Sp
o
el
A
dded initial
i
zation of pbc struct
u
re
before
c
alc_gb
_
for
c
es
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der Spoel
Merge branch 'mast
e
r
'
of git
.
g
romac
s
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-08
Da
v
id van der Spoel
Added
b
o
ndedtype
s
sec
t
ion to rtp
f
iles
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der
S
po
e
l
Re
m
oved po
s
s
i
ble
S
EGVs in rmpbc i
n
case
e
P
BC = N
o
.
commit
|
commitdiff
|
tree
2010-07-08
David van der Spoel
Merge branch 'ma
s
ter
'
o
f
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Dav
i
d van d
e
r Spoel
Merge bra
n
ch
'
master
'
o
f git
.
g
ro
m
acs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Da
v
id v
a
n der Spoel
Fixed misera
b
l
e b
u
g in commrec
.
h where an i
n
t
array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David van der Spoel
F
i
xed bug in
gmx_sumf_com
m
where
a
double
a
rray w
a
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Dav
i
d van der Sp
o
el
Me
r
ge branch 'master' o
f
g
i
t
.
g
r
o
macs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-05
David van der S
p
oel
M
er
g
e branch 'master' of
g
i
t
.
gromacs
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2010-07-05
David van
d
er Spoel
Added sfact
o
r
.
dat to th
e
install
a
tion targets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
Davi
d
van der Spo
e
l
F
ixed
include statements such t
h
at doub
l
e precision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Merg
e
branch 'maste
r
'
o
f g
i
t
.
gromacs
.
o
rg:g
r
oma
c
s
commit
|
commitdiff
|
tree
2010-07-02
David van d
e
r Spoel
Made removi
n
g
p
bc non
-
stati
c
.
T
h
is aff
e
cts
m
any analysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Davi
d
van der Spoel
M
e
r
g
e branch 'master' of gi
t
.
gro
m
acs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van de
r
S
poel
Fixed bug http://bugzilla
.
gromac
s
.
org/show_
b
ug
.
c
gi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van d
e
r Spo
e
l
Fixed http:
/
/
bu
g
zilla
.
gr
o
macs
.
org/show_bug
.
cgi?id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
Da
v
i
d
van der S
p
oel
M
e
rge branc
h
'master'
o
f git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-30
Davi
d
van der Spoel
Fixed bug
in b-fac
t
ors outp
u
t
by
g_confrms
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
v
an der Spoel
Added missin
g
argument step to trotte
r
_upda
t
e
.
H
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Davi
d
van der Spoel
Mer
g
e branch 'master' of gi
t
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid van der Spoel
Updated CMakeLists
.
txt
in ngmx
d
i
rectory to
ex
c
lud
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
v
an der Spo
e
l
Fixe
d
many issues re
g
arding to compi
l
a
tio
n
with
C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van
d
er Spoel
F
ixed Makefile
.
am leadin
g
to warnings
.
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Fix
e
d make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
David van der Spo
e
l
M
e
rge bra
n
c
h 'master' of g
i
t
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-14
David van der S
p
oel
A
d
ded
m
ore fixes in comment
texts, generously provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Da
v
i
d
va
n
der
Spoel
Fixed a lot of spelling er
r
o
r
s in commen
t
s
a
nd
documentat
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
Merge bran
c
h 'mas
t
er' of
git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
Fixed force
fi
e
ld files
f
o
r
A
TP in order to clear bug
commit
|
commitdiff
|
tree
2010-06-10
D
avid van d
e
r Spoel
Merge bran
c
h 'master' of
gi
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-10
David va
n
d
er Sp
o
el
Made legend more or
l
es
s
work in g_chi
.
D
o
n
'
t
know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
d
e
r
S
poel
Fixed SEGV
i
n
g
_chi as descr
i
bed in bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
a
n
der
S
poe
l
Ad
d
ed opt
i
on -nopbc to g_rms
d
ist
in order to
fix
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van
d
er S
p
o
el
Pedanti
c
change i
n
the check whether a f
i
lename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
va
n
der Spoel
Renamed some programs
t
o
f
ollow the
g
_ d
o
c
t
rine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid van
de
r
Spoel
Cle
a
ned up and re
n
amed files in ngmx directory
to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der
Spoe
l
Renamed some files in a
rounda
b
out
way to adh
e
r
e
to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
v
an der Spoel
Rem
o
ved average
.
c, that functional
i
ty is
n
ow in g_analyz
e
.
commit
|
commitdiff
|
tree
2010-06-10
David
van der Spoel
Fixed strange
t
ypo in gmx
_
d
i
h
.
c
commit
|
commitdiff
|
tree
2010-06-06
David van der Spoel
Moved
warn
i
ng mes
s
age in a
d
d_atom
t
ype
to be pr
i
nt
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Dav
i
d v
a
n der Spoel
Made x2top (v
e
ry) slightly fun
c
tional ag
a
i
n
.
S
t
ill
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Davi
d
van
d
e
r
Sp
o
el
Cha
n
ge
d
error messa
g
e
f
or settle
p
robl
e
ms, su
c
h t
h
at
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
A
d
de
d
e
xplicit angle in ACE decla
r
a
tion
i
n gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
i
d
van der
S
po
e
l
Fixed type in gm
x
_morph
.
c: e
f
TRO -> efTRX w
h
ic
h
lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fixed bug 39
6
.
I
n f
a
ct it w
a
s
alr
e
ady fixed pa
r
tly
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fixed bug
401 by implementing the
pr
o
posed
p
atc
h
that
.
.
.
commit
|
commitdiff
|
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