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Fixed documentation text according to bugzilla 486
2010-08-03
David
van der Spoel
Fixed documentation
t
ext
a
cc
o
rding to bugzilla 486
commit
|
commitdiff
|
tree
2010-08-01
David
v
an der Spoel
Me
r
ge br
a
nch 'release-4-5-pat
c
hes' of git
.
g
roma
c
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David van d
e
r S
p
oel
Mov
e
d
p
d
b
2top
.
h from
src/kernel to
i
ncl
u
d
e
to al
l
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van der Sp
o
el
Renamed t
y
pename to my_typ
e
name
in ind
e
x
.
c sinc
e
typ
e
nam
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David v
a
n der S
p
o
e
l
F
ixed compilat
i
on issue corresp
o
nding to bug 468
commit
|
commitdiff
|
tree
2010-07-14
David van der Spo
e
l
Fixed bug 467 realting t
o
pdb2gmx
outp
u
t
of
t
he water
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van d
e
r Spoel
Added citation for
s
c
attering facto
r
s
.
Us
e
d in g_rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
Add
e
d mo
r
e
at
o
ms to th
e
scattering
f
a
ctor data file
.
commit
|
commitdiff
|
tree
2010-07-14
David van der
Spo
e
l
Fixed bug
462
.
pdb2gmx
s
hould now p
r
oduc
e
the
c
orrect
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
David van der Spoel
F
ixed b
u
g
4
66 by co
m
m
e
nting
out the offend
i
ng lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
D
a
vid van der Spoe
l
Merg
e
branch 'mas
t
er'
o
f
git@git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d
van der Spoel
Ad
d
ed in
i
tializati
o
n of pbc struct in genborn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
David van d
e
r Spoel
Adde
d
initialization of pbc structure be
f
ore calc
_
gb_f
o
rces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d van der Spoel
M
erge branch 'm
a
s
t
e
r
'
o
f
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d
van d
e
r Spoel
A
dd
e
d bo
n
dedt
y
pes
s
e
ction to rtp files
.
I
t
might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David
van der S
p
oe
l
Removed po
s
sible SEGVs in r
m
pb
c
in case ePB
C
= No
.
commit
|
commitdiff
|
tree
2010-07-08
Da
v
id
v
an der Spoel
Me
r
ge branch
'
m
a
ster' of git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-07
David va
n
der Spo
e
l
Merge branc
h
'm
a
ster' o
f
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Dav
i
d van der Spo
e
l
Fixed miserable
b
ug in commrec
.
h where an int array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David van der Spoel
F
ixed bug in gm
x
_sumf_comm where
a
double
array was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David van d
e
r Sp
o
el
Merge bra
n
ch 'ma
s
ter' of git
.
g
r
omacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-05
D
avi
d
van der Spoel
Merge b
r
anch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
D
avid van der Spoel
A
dd
e
d sfactor
.
d
at to the insta
l
lation targets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
David van d
e
r Spoel
Fixed
include statement
s
such th
a
t double pre
c
ision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van
d
er Spoel
M
e
rge branch 'ma
s
t
er' of git
.
gro
m
a
c
s
.
o
r
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Made r
e
moving pb
c
n
o
n-static
.
This affects ma
n
y ana
l
ys
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Dav
i
d van de
r
Spoel
Merge branch 'master' o
f
g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
D
avid van
d
er Sp
o
e
l
Fixed bug htt
p
://bugzi
l
la
.
g
romacs
.
org
/
show_
b
ug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van de
r
Spoel
Fixed h
t
t
p://bugzilla
.
gromacs
.
org/show_
b
u
g
.
cgi
?
i
d
=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van der Spoel
Merge
b
ran
c
h 'ma
s
ter' o
f
git
.
groma
c
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-06-30
Dav
i
d van der Spoe
l
Fixed
bug in b-fa
c
tors output by g_conf
r
m
s
.
T
hey wer
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
Added missing
a
rg
u
ment step to
t
rotter
_
up
d
ate
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van der Spoel
Merge
branc
h
'master' of
git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-06-27
Dav
i
d
van der Spoel
Updated CMakeLists
.
txt in
n
gmx directory
to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van der Spoel
Fixed many issues
r
ega
r
ding
t
o compilation with C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der Spoel
Fi
x
ed Makefil
e
.
am le
a
ding
t
o
war
n
i
n
gs
.
commit
|
commitdiff
|
tree
2010-06-14
Da
v
id va
n
der
S
poel
Fi
x
ed
m
ake_e
d
i
.
c
commit
|
commitdiff
|
tree
2010-06-14
David v
a
n
d
e
r
Spoel
Merge branch 'ma
s
ter' of git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-06-14
Dav
i
d van der Spoel
Added more fixes in comment
t
exts, generously prov
i
ded
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
David van
der Spoel
Fixe
d
a
l
ot of spelling errors in comments and document
a
tion
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David
van der Spoe
l
Merge branch 'master' of git
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David
v
an der Spoel
Fixe
d
force f
i
eld files for
A
TP in
o
r
der to clear
b
ug
commit
|
commitdiff
|
tree
2010-06-10
David van der
S
poel
Mer
g
e
branc
h
'mas
t
er' of gi
t
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-10
David
v
a
n
der
S
poel
Made
l
egend more
or
le
s
s
work in
g
_chi
.
D
o
n'
t
know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David va
n
de
r
Spoel
Fix
e
d
SEGV in g_chi
a
s described in
b
ug 430
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
i
d van der Spoel
Ad
d
ed option
-
n
opbc to g_rms
d
i
s
t in
orde
r
to
fix
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
P
e
dantic c
h
a
nge
in the check
whether a filename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der
Spoel
Renamed some programs to follow the g
_
doct
r
in
e
:
l
u
ck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Cleaned up and renamed files i
n
n
gmx
d
ir
e
ctory
to
b
etter
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d v
a
n
der Sp
o
e
l
Renamed
some files i
n
a roundabout way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der
Spoel
Removed ave
r
a
ge
.
c,
t
hat
f
unctionality
is now i
n
g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der Spoel
Fixed strange typo
i
n gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David va
n
der Spoel
M
oved w
a
rning m
e
s
sag
e
i
n
add_a
t
o
m
ty
p
e to be printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David v
a
n der Spo
e
l
Made x
2
top (
v
e
r
y
)
slight
l
y functio
n
al again
.
Still
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
van d
e
r Spoe
l
Changed error message for settle p
r
oble
m
s, such that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
d
er Spoel
Added explicit angle in
A
CE
d
eclara
t
ion
i
n gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
i
d van der Spo
e
l
Fixed type in gm
x
_morp
h
.
c: efTRO -
>
e
fTRX which
l
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
de
r
S
poel
F
i
xed bug
396
.
In
fact it was already fixed
partly
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
a
n der Sp
o
el
F
ixed bug
401 b
y
implementing the proposed
patc
h
t
h
at
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id
van der Spoel
F
ixed bug 381 b
y
adding the nu
m
ber of
the
f
irst ato
m
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van de
r
Spoel
F
ixed bug 349
.
The f
i
le made with the -vis option has
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
M
erge branch 'master' of gi
t
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-02
David van
der Spoel
Removed option CAN_DT f
r
om g_msd, since it ca
n
not
h
andle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
avid
v
an d
e
r Spoel
Increa
s
ed buffer size for reading in a whole
fil
e
at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Davi
d
van der Sp
o
el
Merge branch 'ma
s
ter' of git
.
g
r
omacs
.
o
r
g:
g
romacs
commit
|
commitdiff
|
tree
2010-05-25
David van der Spoel
Added one more!
commit
|
commitdiff
|
tree
2010-05-24
D
a
vid v
a
n der
S
p
o
el
Removed C++ style comments
in mdrun
.
commit
|
commitdiff
|
tree
2010-05-21
Dav
i
d
van der Spoel
Fix
e
d compilation
w
a
rnings
a
nd removed spurious
C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
David van der Spoel
Added 1
commit
|
commitdiff
|
tree
2010-05-20
David van
d
e
r
Spoel
Made g_analyze comp
i
le again
,
b
u
t ot lin
k
yet
.
commit
|
commitdiff
|
tree
2010-05-19
Da
v
id
van
der Spoel
M
erge branch 'master'
o
f
g
it
.
gr
o
m
a
cs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-05-19
D
avid va
n
der Spoel
Added check in read_pdb for existence of t_r
e
s
i
n
fo
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
Da
v
id van der Spo
e
l
Add
e
d
a
c
ool
q
u
ote,
and rem
o
ved two
comma's in op
e
nmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David va
n
d
e
r Spoel
Merge branc
h
'ma
s
ter'
o
f
git
.
gromac
s
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-05-16
D
avid
v
an
d
er Spoel
Fixed scattering funct
i
on c
o
de
in g_rdf
.
A new fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Spo
e
l
Added mul
t
i regr
e
ssion analysis
to g_analyze
.
See
i
nfo
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
Fixed compilati
o
n issue
i
n g
e
m
inate
.
c
d
ue to non-defined
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Sp
o
el
Merge branch '
m
as
t
er' o
f
git@git
.
gr
o
mac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
D
a
vid van de
r
Spoel
Merg
e
branch 'master' of git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-05-12
David v
a
n
der Spoel
Del
t
ed two mo
r
e
s
uper
f
luous
files
commit
|
commitdiff
|
tree
2010-05-11
David
v
a
n
der Spoel
C
l
eaned up in top directory
.
Moved a few old itp
f
i
les
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
David van
der Spoel
Move
d
p
hosphate files into gmx
.
ff direc
t
o
r
y
.
commit
|
commitdiff
|
tree
2010-05-11
David van
der Sp
o
el
Mov
e
d propanol itp file
t
op oplsaa
.
ff,
removed t
w
o
.
.
.
commit
|
commitdiff
|
tree
2010-05-02
Davi
d
van de
r
S
p
oel
M
e
r
g
e bra
n
ch 'master' of g
i
t@git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-04-30
David
van der Spoel
A
dded one
commit
|
commitdiff
|
tree
2010-04-26
D
a
vid v
a
n der Spoel
M
a
de his
t
ogramming slight
l
y more flexible
.
Used in
.
.
.
commit
|
commitdiff
|
tree
2010-04-12
Davi
d
van d
e
r
S
p
oel
Merge branch 'm
a
ster' of
git@gi
t
.
gromac
s
.
or
g
:g
r
omacs
commit
|
commitdiff
|
tree
2010-04-12
David va
n
der Spoel
Changed the output of topology
files t
o
i
nclude the
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
David van der Spoel
Me
r
ge branch 'master' of g
i
t@git
.
g
r
om
a
cs
.
or
g
:gro
m
acs
commit
|
commitdiff
|
tree
2010-04-06
D
avi
d
van der Spoe
l
Added st
a
t
ement to set rt
p
t
o NULL
.
commit
|
commitdiff
|
tree
2010-04-06
D
a
vid van der Spoel
Revert
"
Added argument rt
p
name
to
t
_atoms_set_
r
esinfo
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
D
a
vid van der
S
poel
Added
a
rgu
m
ent rtpname to t_atoms_
s
e
t_resinfo
to avoid
.
.
.
commit
|
commitdiff
|
tree
2010-04-04
David van der Spoel
Added one
.
commit
|
commitdiff
|
tree
2010-04-04
David
v
an de
r
Spoel
Merge branc
h
'master
'
o
f
git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-03-31
David van der Spoel
Added one
commit
|
commitdiff
|
tree
2010-03-12
D
a
vi
d
v
an der Spoel
Merge branc
h
'ma
s
ter' of git
.
g
r
omacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-03-12
David
v
an der
S
poel
Adde
d
flush
a
f
te
r
writing to
d
ebug file
commit
|
commitdiff
|
tree
2010-03-11
Dav
i
d v
a
n der Spoel
Aded function co
p
y_t_atoms,
u
pdated functio
n
add_t_atoms
.
.
.
commit
|
commitdiff
|
tree
2010-03-10
D
a
vid van der Spoel
Merge b
r
anch
'
mast
e
r
'
of git@git
.
groma
c
s
.
org:g
r
omac
s
commit
|
commitdiff
|
tree
2010-03-10
D
a
vid van der Spoel
Added routine ad
d
_t_atom
s
to
increa
s
e the length of
.
.
.
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|
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