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Added initialization of pbc structure before calc_gb_forces was called from
2010-07-09
Da
v
id van d
e
r Spoel
A
dded in
i
t
i
a
lization
of
p
bc
structure before calc_gb_forces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van der Sp
o
el
M
e
r
g
e branch '
m
aster' of git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-08
Dav
i
d v
a
n
d
er Spoel
Adde
d
b
o
n
dedtypes section to rtp files
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
Davi
d
van der Spoel
Remove
d
p
o
s
sib
l
e
SEG
V
s
i
n
r
m
pbc in c
a
se ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
David van d
e
r Spoel
Merge branch 'm
a
ster'
of git
.
g
r
omacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-07
D
avid
v
an de
r
Spoe
l
Merge
b
r
anch '
m
aste
r
'
o
f
git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-07
Davi
d
v
a
n
d
er
Spoel
Fixed miserable bug
i
n c
o
mmre
c
.
h where an in
t
array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
D
a
vid van der Spoel
Fixe
d
bug in gmx_sumf_comm whe
r
e
a
double ar
r
ay was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Da
v
i
d
van der Spoel
Merge
branc
h
'm
a
ster' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
David
van der Spoel
M
erge branch 'master' of
git
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-05
David van de
r
Spoe
l
A
dded
sfactor
.
dat to th
e
insta
l
lation
targe
t
s in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
D
a
vid van de
r
S
p
oel
Fix
e
d include
statem
e
nts such
t
hat doubl
e
precision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van d
e
r Spoel
M
erge
b
ranch 'master' of git
.
gromacs
.
o
r
g:
g
romacs
commit
|
commitdiff
|
tree
2010-07-02
Da
v
id van d
e
r S
p
oel
Made
removing
pb
c
n
on-st
a
t
i
c
.
This affect
s
man
y
a
n
alysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Da
v
id van der Spoel
Merge branch 'master' of git
.
gr
o
ma
c
s
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-02
D
a
v
id van de
r
S
p
oel
Fix
e
d bug http://
b
ugzilla
.
g
r
omacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van
der Sp
o
el
F
i
xed h
t
tp://bugzill
a
.
g
romacs
.
org/show_bug
.
c
g
i?i
d
=
4
57
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David van
d
er Spoel
Merge branch
'
master' o
f
git
.
g
r
o
m
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-30
Davi
d
van der S
p
oel
F
ixed bug
i
n
b-
f
a
c
t
ors output by g_con
f
rms
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David va
n
der Spoel
Added
m
issing
argument
s
t
e
p to trotter_up
d
ate
.
H
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
Merge branch 'master' of git
.
gromacs
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoe
l
Updated CM
a
keLists
.
txt in ngmx directory to
e
xclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spo
e
l
Fixed many
is
s
ues re
g
arding to c
o
mpi
l
ation
w
it
h
C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der Spo
e
l
Fixed
M
a
ke
f
ile
.
am leadin
g
to warnings
.
commit
|
commitdiff
|
tree
2010-06-14
D
a
vid v
a
n de
r
Spoel
Fixed mak
e
_ed
i
.
c
commit
|
commitdiff
|
tree
2010-06-14
D
avid van d
e
r Spoel
Mer
g
e branch 'master'
of git
.
gro
m
acs
.
or
g
:
grom
a
cs
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Added
m
ore fixes
in comment texts, generously provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Da
v
id van der Spoel
Fixe
d
a lot
of
spelling erro
r
s i
n
comments a
n
d documentati
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
David
va
n
d
e
r Spoel
Merge br
a
nch '
m
aster' o
f
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
Fixed for
c
e field
file
s
for
A
TP in
o
rder
to cl
e
ar bug
commit
|
commitdiff
|
tree
2010-06-10
D
av
i
d
van der Spoel
Merge branch 'master'
o
f git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-10
David v
a
n der Sp
o
el
M
ade
legend mo
r
e
o
r less wo
r
k in g_
c
hi
.
Don't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Fixed
S
EGV in g_chi as descr
i
be
d
in bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van
d
er Spoel
Added option
-nopbc to g_rmsdist in order
to fix
commit
|
commitdiff
|
tree
2010-06-10
David van
d
er Spoel
P
edantic change in the check whether a f
i
lename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Renam
e
d some programs to follow
t
he g_ doctrine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
C
le
a
ned up an
d
re
n
amed files in ngmx dir
e
ctory
t
o
better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van de
r
Spoel
Ren
a
med so
m
e files in a rounda
b
out way to ad
h
er
e
t
o
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Removed a
v
erage
.
c
,
tha
t
funct
i
onality is now in g
_
analyze
.
commit
|
commitdiff
|
tree
2010-06-10
David v
a
n der
S
p
oel
F
i
xed strange
typo
i
n gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David
v
a
n
der
S
poel
Moved
war
n
i
n
g messag
e
in add
_
atomty
p
e
to
be prin
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Dav
i
d van
d
er
S
poel
Made x2top
(very)
s
ligh
t
ly functi
o
nal again
.
S
til
l
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id va
n
d
er S
p
oel
Changed error message fo
r
settle problems, such
that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Davi
d
va
n
der Spoe
l
A
d
ded explici
t
angle in ACE decl
a
ration in gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid van der Spoel
Fixe
d
ty
p
e in gmx
_
m
o
rph
.
c: efTRO -> efTRX whic
h
lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
an der Spoel
Fixed bug 396
.
In fact it was already fixed
p
artly
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
an der Spoel
Fixed bug 401 by
im
p
l
ementing the
proposed patch that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Sp
o
el
Fixe
d
bug 3
8
1 by adding t
h
e
n
umber
o
f
t
he f
i
rs
t
atom
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David v
a
n de
r
Sp
o
el
Fixed bug
3
4
9
.
The file made with t
h
e
-vis opt
i
on
h
as
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid van
der Spoel
Merge branch 'maste
r
' of g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d van der Spoel
Remo
v
ed
o
ptio
n
CAN_DT from
g
_msd,
since
i
t
cannot handle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d van der Spoel
Increased buffer
size for readin
g
in a whole
f
ile at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
David van der Spoel
M
erge br
a
nch 'master'
of git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-05-25
Dav
i
d van der
Spoel
A
dded on
e
m
o
r
e!
commit
|
commitdiff
|
tree
2010-05-24
D
avid
v
an der
Spoe
l
Remov
e
d
C
++ s
t
yle
c
omments in mdr
u
n
.
commit
|
commitdiff
|
tree
2010-05-21
Dav
i
d van d
e
r Spoel
Fixed
c
ompi
l
atio
n
war
n
ing
s
and r
e
moved spur
i
ou
s
C
+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
David v
a
n der S
p
oel
Adde
d
1
commit
|
commitdiff
|
tree
2010-05-20
David va
n
de
r
Spo
e
l
Made g_a
n
alyz
e
co
m
p
i
le
a
gain
,
but ot link yet
.
commit
|
commitdiff
|
tree
2010-05-19
David van
d
er S
p
o
el
Me
r
ge b
r
anch 'master' of git
.
gromacs
.
or
g
:groma
c
s
commit
|
commitdiff
|
tree
2010-05-19
David van der Spoel
Added check in read
_
pdb for e
x
istence of t_resinfo
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
David van
der Sp
o
el
Added a coo
l
q
uote,
a
nd
removed tw
o
co
m
ma
'
s
in
o
p
enm
p
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Da
v
id
van
der Spo
e
l
Me
r
ge branch 'mast
e
r
' of git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-05-16
D
avi
d
van der Spo
e
l
F
ixed
s
cattering functio
n
code in g_
r
df
.
A
new file
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van d
e
r Spoel
A
dded
multi regression analysis to g_analyze
.
See info
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
D
a
vid
v
a
n
d
e
r S
p
oel
F
i
xed c
o
mpil
a
tion issue in geminate
.
c due to no
n
-defined
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
Merg
e
branch 'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
David van der Spo
e
l
M
e
rge branch
'master' o
f
g
i
t
.
grom
a
cs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-05-12
David v
a
n der S
p
oel
Delted
t
wo
more su
p
erf
l
uou
s
files
commit
|
commitdiff
|
tree
2010-05-11
Dav
i
d van der Spoel
Cle
a
ned up in to
p
dire
c
tory
.
Moved
a
few old i
t
p files
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
Da
v
id
v
an der Spo
e
l
M
ov
e
d
ph
o
sph
a
te files into gmx
.
ff directory
.
commit
|
commitdiff
|
tree
2010-05-11
David van der Spoel
M
o
ved propanol itp file top opls
a
a
.
ff, remo
v
ed two
.
.
.
commit
|
commitdiff
|
tree
2010-05-02
David van der Sp
o
el
Merge branch 'ma
s
ter' of git@g
i
t
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-04-30
David van der Sp
o
e
l
Added one
commit
|
commitdiff
|
tree
2010-04-26
David va
n
d
e
r Spoel
Ma
d
e histogramming slight
l
y
m
ore flexible
.
Use
d
in
.
.
.
commit
|
commitdiff
|
tree
2010-04-12
David v
a
n der Spoel
Merge
b
ranch 'ma
s
ter'
o
f git@git
.
groma
c
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-04-12
D
a
vi
d
van der Spoel
C
han
g
ed the outpu
t
of to
p
ology files to include
t
he
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
Davi
d
van d
e
r Spoel
Merge branch
'
master' of git@git
.
groma
c
s
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-04-06
D
avid van der Spoel
Added
s
tatement t
o
set rtp
t
o NUL
L
.
commit
|
commitdiff
|
tree
2010-04-06
David van der Spoel
Revert "
A
dded
a
rg
u
men
t
r
t
p
name to t_atoms_
s
et_re
s
info
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
David van d
e
r
Spoel
Added argum
e
n
t
rtpna
m
e t
o
t_atoms_set
_
resinfo to avo
i
d
.
.
.
commit
|
commitdiff
|
tree
2010-04-04
David
v
an der Spoel
Added one
.
commit
|
commitdiff
|
tree
2010-04-04
David van der Spoel
M
e
rge b
r
anch 'maste
r
' of git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-31
D
a
vi
d
van der Spo
e
l
Added one
commit
|
commitdiff
|
tree
2010-03-12
D
a
vid van der Spoel
M
e
rge branch
'
m
a
ste
r
' of
g
it
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-03-12
Da
v
id
v
an der Spoel
Added flush after writing to debug file
commit
|
commitdiff
|
tree
2010-03-11
David va
n
der Spoel
Aded function copy_t_atoms, upd
a
te
d
fun
c
t
ion add_t_
a
t
o
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-03-10
David
v
a
n der S
p
oel
Merge b
r
a
n
ch 'master' of git@git
.
groma
c
s
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-03-10
David van d
e
r Spoel
Added ro
u
t
i
ne add_t_at
o
ms
t
o incr
e
a
se
t
h
e length of
.
.
.
commit
|
commitdiff
|
tree
2010-02-15
David van
d
e
r
Spoel
U
p
da
t
e
d
commit
|
commitdiff
|
tree
2010-02-14
David van der Spoel
Added function to
i
ncrease
t
he ar
r
ay size
s
in a
t
_at
o
ms
.
.
.
commit
|
commitdiff
|
tree
2010-02-13
D
a
vi
d
van der Spoel
Replaced some str
c
py by strncpy to avoid
o
ver
f
lows
.
commit
|
commitdiff
|
tree
2010-02-09
Davi
d
v
a
n der Spoel
Merge
b
ranch 'master' of git@git
.
grom
a
cs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-02-09
David va
n
der Spoel
Added an e
m
p
t
y line to share/
h
t
m
l/Makefil
e
.
a
m to fool
.
.
.
commit
|
commitdiff
|
tree
2010-02-06
Dav
i
d
v
an
d
er Spoel
Fi
x
ed h
t
mldi
r
stuff
.
commit
|
commitdiff
|
tree
2010-02-06
David va
n
der Spoel
Replaced two strcpy by st
r
ncpy in pdbio
.
c to prevent
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
David van der Spoel
C
o
nfigure n
o
w
u
ses the
-
-htmldir op
t
ion
.
commit
|
commitdiff
|
tree
2010-02-05
David van der
Spoel
Configure now uses the
-
-htmldir option
.
commit
|
commitdiff
|
tree
2010-02-05
D
a
vid va
n
der Spoel
Merge branch 'm
a
s
te
r
'
o
f
git
.
g
romacs
.
or
g
:grom
a
cs
commit
|
commitdiff
|
tree
2010-02-03
David van der
S
po
e
l
R
emoved FF
.
dat
from share
/
top/
M
akefi
l
e
.
a
m
commit
|
commitdiff
|
tree
2010-02-01
David van der Spoel
Merge b
r
anch
'
master'
o
f git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
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