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Fixed more PBC and indexing stuff.
2011-01-30
David van
d
er Spo
e
l
F
i
xed more PBC and indexi
n
g stuff
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
F
ixed
t
ypo
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
v
an der Sp
o
el
Merge b
r
anch 'releas
e
-4-5-patches' into o
r
derparm
commit
|
commitdiff
|
tree
2011-01-29
David
v
an de
r
Spoe
l
Me
r
ge branch 'release
-
4-5-
p
atches' of git
@
g
i
t
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
David van d
e
r
S
poel
Add
e
d
c
ode
i
n
g_nmeig to com
p
ute the
qua
n
tum corre
c
tions
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David van d
e
r
S
poel
Merge
bra
n
ch 're
l
ease-4-5-pa
t
ches'
o
f
git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David v
a
n
d
er S
p
oel
Fixed
bug
678 which
was
due to
c
alling gmx_f
a
t
al without
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
David van der Spoel
Merge
branch
'release-4-5-patches' of git
@
git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van der Spoe
l
Added
w
a
r
n
i
ng in
g_
d
ipol
e
s
commit
|
commitdiff
|
tree
2010-12-23
D
a
vid v
a
n
der
S
poel
Fixed bug in sta
t
istics whi
c
h did not allow fitting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David
van der Spoel
Merge b
r
anch 'releas
e
-4-5-patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
avid van der Spoel
Added 1
q
uote
.
commit
|
commitdiff
|
tree
2010-12-09
David v
a
n der Spo
e
l
Added fatal err
o
r for when people
u
se energy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
D
a
vid van
der Spoel
Fixed bugzil
l
a
616 abou
t
formatting in
t
h
e
help t
e
xt
.
commit
|
commitdiff
|
tree
2010-11-26
Dav
i
d van der Spoel
Fi
x
ed S
E
GV bug in g
_
sh
a
m
.
commit
|
commitdiff
|
tree
2010-11-18
David van der Spoel
Made prin
t
ing in
check_mu
l
ti_in
i
t co
n
ditional, dep
e
n
ding
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
David van der Spo
e
l
Fixed bug 60
8
by t
h
rowing a
fatal err
o
r in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
David
v
an de
r
Spo
e
l
Merge bran
c
h 'release-4-5-patch
e
s' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David van der Spoel
Mer
g
e b
r
a
n
ch 'release-4-5-pa
t
ches'
o
f git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
D
avid van
der Spoel
Fixed compi
l
ation issues wit
h
C99 compatibility
.
commit
|
commitdiff
|
tree
2010-10-07
David van der
Spoel
Fixes a
n
d small additions t
o
g_wham, due to Jochen
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David van der Spo
e
l
Re-added g_
k
inetics to src/tools/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
David van der
S
p
oel
Added s
o
ftware-related quote
commit
|
commitdiff
|
tree
2010-09-24
David van der
Spoel
Updated to ref
l
e
c
t
bug 557
.
commit
|
commitdiff
|
tree
2010-09-20
Dav
i
d van der Spo
e
l
Me
r
ge branch 'rel
e
ase-4-5-patches' of git@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
David van d
e
r Spo
e
l
Fixed bug http://bugzilla
.
gromacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
David
v
a
n der Spoel
Co
r
rect
e
d name of one of the developers li
s
ted i
n
h
eader
.
commit
|
commitdiff
|
tree
2010-09-14
David van der Spoel
F
i
xed bug
5
5
3
by ch
e
cking whe
t
her
a
n atom
name is longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
Dav
i
d van der Spoel
Fixed dem
o
to work
w
i
th new pdb2gmx that r
e
quires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Dav
i
d van der Spoel
Made genrestr -cons
t
r to
p
r
o
duce con
s
traints of type
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Davi
d
van der Spoel
F
i
xed bug 417
.
commit
|
commitdiff
|
tree
2010-08-19
D
avid van d
e
r Sp
o
e
l
Fixes more mis
e
ry in
f
unct
i
on skipstr,
wh
e
re poin
t
er
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Ad
d
ed
t
wo missing include fi
l
e
s
.
Fixed ho
r
r
i
bl
e
coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
D
a
vid van der Spoel
Fi
x
ed reuse of
v
ariable
a
s te
m
p
va
r
iable before printi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David v
a
n der Spoe
l
Fixed bug 487 accordi
n
g
to provided pat
c
h
.
commit
|
commitdiff
|
tree
2010-08-03
D
a
vid van der Spo
e
l
Fixed doc
u
menta
t
i
o
n
t
ext according to bug
z
illa 486
commit
|
commitdiff
|
tree
2010-08-01
David v
a
n der Spoel
Merge branch '
r
elea
s
e-4-5-patches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David
van der Spoel
Moved pdb2top
.
h from
src/kernel to include to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
D
avid van der
S
poel
Rena
m
ed
t
ypename t
o
my_typename in
index
.
c since type
n
ame
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David van
d
er Sp
o
el
Fi
x
ed compilation issu
e
cor
r
esponding to bug 468
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
Fixed
bug 467
realt
i
ng to p
d
b2gmx output
of the
w
ater
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
D
a
vid
v
an der Sp
o
e
l
Added cit
a
tion
for s
c
atter
i
ng factors
.
U
s
ed
in g_rdf
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David
v
an d
e
r Spoel
Added mo
r
e
atoms to the scattering factor da
t
a file
.
commit
|
commitdiff
|
tree
2010-07-14
Davi
d
van der
S
poel
Fi
x
ed bug
4
62
.
pd
b
2gmx shou
l
d now produce th
e
correct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
David van der Spoel
Fixed
b
ug 466 by
c
ommenting out the offending lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David
v
an der S
p
oel
Merge branch 'mast
e
r' of git@
g
it
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-12
David van der
S
poel
Added i
n
itiali
z
ation of
pbc str
u
ct i
n
genborn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
D
avid va
n
der Spo
e
l
A
d
ded in
i
tializatio
n
of p
b
c
st
r
ucture
b
efore calc_gb_
f
o
rces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David
v
an der Spoel
M
er
g
e
b
ranch 'mast
e
r' of git
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-08
Da
v
id van der Sp
o
el
Added
bondedtypes section to rtp
files
.
It
might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David v
a
n der
S
p
oel
Rem
o
ved
p
ossible SEGV
s
in rmpbc in case ePBC =
N
o
.
commit
|
commitdiff
|
tree
2010-07-08
Davi
d
van der
Spoel
Me
r
ge branch '
m
as
t
er' of
git
.
gromacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-07
D
a
vid van de
r
Spoel
Me
r
ge branc
h
'ma
s
ter' of git
.
g
romacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-07-07
Dav
i
d va
n
d
er Spoel
Fixed miserable
b
u
g
in commrec
.
h
where an int array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
David van der S
p
oe
l
Fixe
d
bug in
g
mx_sum
f
_c
o
m
m where a double array was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David van der Sp
o
e
l
M
erge bra
n
ch 'm
a
ster' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
David
van
der Spoel
Merge branch 'm
a
ster' of git
.
g
romacs
.
or
g
:gro
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-05
Davi
d
van der Spoel
Added sfactor
.
dat
to
the insta
l
l
atio
n
t
a
rgets in share
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
David van der Sp
o
el
Fixed i
n
clu
d
e statem
e
n
t
s such that dou
b
le preci
s
io
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David
v
an d
e
r
Spoel
Merge bran
c
h
'master' of git
.
g
romacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Made remov
i
ng pbc non-st
a
t
i
c
.
Thi
s
aff
e
cts many ana
l
ys
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
David van der
S
poel
Merge
b
ranch
'
master' of git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
David van der Spoel
Fixed bug http:/
/
bugzil
l
a
.
gromacs
.
or
g
/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
D
avid va
n
der Spoel
Fi
x
ed http:
/
/bugzilla
.
grom
a
cs
.
org/sh
o
w_b
u
g
.
cgi?
i
d=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David
van d
e
r Spoe
l
Merge branch 'master' o
f
git
.
g
r
omac
s
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-30
Dav
i
d va
n
der Spoel
F
ix
e
d bug in b-fa
c
to
r
s
output by g_conf
r
m
s
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
D
a
vid van der Sp
o
el
Added m
i
ssin
g
argument step to trotter_
u
pdate
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
M
e
r
ge branch 'master' of gi
t
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-27
David van der S
p
oel
U
p
dated
CMakeLi
s
ts
.
txt in ngmx director
y
t
o excl
u
de
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der Spoel
Fi
x
ed ma
n
y is
s
u
e
s reg
a
rding to
c
omp
i
latio
n
with
C
+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van d
e
r Spoel
Fixed Makefile
.
am leading to warnings
.
commit
|
commitdiff
|
tree
2010-06-14
Da
v
id van der Spoel
Fixed make_ed
i
.
c
commit
|
commitdiff
|
tree
2010-06-14
David
van der Sp
o
e
l
Merg
e
b
ranch '
m
aster' of git
.
g
romacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van
d
e
r
S
p
o
el
Added
m
ore
fi
x
es in
comme
n
t texts,
g
e
n
er
o
usly provided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
David van der
S
poel
Fixed a l
o
t o
f
spelling errors
in comments and
d
ocumenta
t
ion
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
D
a
vid van der Spo
e
l
M
e
rge br
a
nch 'm
a
ste
r
' of git
.
g
romacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David van der Spoel
Fixe
d
force field fi
l
es f
o
r ATP
in
or
d
er
to
clear bug
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid v
a
n
de
r
Spoel
Merge branch 'mast
e
r' of
g
it
.
gromacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2010-06-10
David van de
r
Sp
o
el
Made legend more or
l
ess
work in
g
_chi
.
D
o
n't
k
now
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
d
er Spoel
Fix
e
d
SEGV in g_chi a
s
d
e
s
cribed i
n
b
ug 430
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spo
e
l
Added opt
i
on -n
o
pbc to g_rmsd
i
st in order to fix
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der Spoel
Pedantic change in the c
h
e
c
k wheth
e
r a filename
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
vid v
a
n
d
er
S
p
o
el
Renamed so
m
e programs to foll
o
w the g_ doctrine: lu
c
k
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoe
l
Cleaned
up
a
nd r
e
named
f
iles in ngmx directory to bette
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van der Spoel
Renamed som
e
files in
a rounda
b
out way to adhere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoe
l
R
emoved av
e
rage
.
c, t
h
at
functio
n
ality is no
w
in g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der Spo
e
l
Fixed strange
t
ypo in gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David van der Spoel
Moved war
n
ing message in add
_
atomty
p
e to be printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David
v
an der S
p
o
el
M
a
de x2top (ve
r
y) slightly
f
unctional again
.
Still
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spo
e
l
Cha
n
ged e
r
ro
r
message for settle prob
l
ems
,
such that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der
Spoe
l
Added explic
i
t angle in
ACE declar
a
tio
n
in gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fi
x
ed type in
g
mx_morph
.
c: efT
R
O -> efTRX
w
hich
l
ead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid van d
e
r S
p
o
e
l
Fixed b
u
g 396
.
I
n fact it was alread
y
fi
x
ed pa
r
tly
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fixed
b
u
g 401 by implementing t
h
e p
r
opo
s
e
d
pat
c
h
that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Davi
d
van de
r
Spoel
Fi
x
ed bug 381 by a
d
din
g
the number
o
f the first atom
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vid
v
an
d
er
S
poel
Fixed
b
ug 349
.
The file made
w
ith
the -vis op
t
ion
h
as
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van d
e
r Spoel
Merge branch
'mast
e
r' of
git
.
g
romacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-02
David van
d
e
r
S
p
o
el
Rem
o
ved
op
t
ion C
A
N_DT
f
rom
g
_msd, since it c
a
nnot
handle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
van der Spoel
Incre
a
s
e
d buffer size for readi
n
g in a
whole
f
ile at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
David
van der Spo
e
l
Merge
b
ranch
'master
'
of gi
t
.
gromacs
.
org:gromacs
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