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Merge "changed number of iatoms for F_SETTLE from 1 to 3" into release-4-6
2012-04-29
Dav
i
d van der Spoel
M
e
rge "chan
g
e
d numb
e
r of iatoms for F_SETTLE from 1
.
.
.
commit
|
commitdiff
|
tree
2012-04-29
David van der Spoe
l
Merge "add
e
d support f
o
r g
r
aphs n
o
t sta
r
ting a
t
0"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
David
van der Spoel
Merg
e
"[tool
s
] g_sans
- splited out fixes and added
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Dav
i
d v
a
n
d
er Spoel
Mer
g
e
"Various imp
r
ovements to
s
hell co
d
e" in
t
o release
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
David van der S
p
oel
Mer
g
e "Adde
d
su
p
port for dssp2
.
X with the -ver option
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
D
avid van der Sp
o
el
M
e
rge "Expanded the help
t
ext regardin
g
t
h
e -
r
2
a
nd
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
David va
n
der Spo
e
l
Merge
"
I
mproved
pdb2gmx error mess
a
g
e" into release
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
Da
v
id van
d
er Spoel
Merge
"
F
i
x typo in Cl
a
n
g CFlags
"
into relea
s
e-4
-
5
-
patches
commit
|
commitdiff
|
tree
2012-03-18
David v
a
n der Spoel
Merge "
M
er
g
e release-4-
5
-patc
h
es
i
nto release
-
4-6
"
.
.
.
commit
|
commitdiff
|
tree
2012-03-17
David van der Spoel
R
emoved qho
p
files fr
o
m this
br
a
nch
.
commit
|
commitdiff
|
tree
2012-03-10
D
a
vid van
d
er Spoel
Vibration spectra from velocity ACF or Normal modes
.
commit
|
commitdiff
|
tree
2012-03-09
Dav
i
d v
a
n
der S
p
oel
Merge "Impro
v
e
d
c
ryptic error mess
a
ge"
i
n
t
o release
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
Davi
d
van der S
p
oel
Merge "M
i
nimal su
p
po
r
t
for
C
la
n
g
" into re
l
ease
-
4
-
5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
D
a
vi
d
van der Spoel
M
erg
e
"
M
ino
r
form
a
tting fixes to
.
mdp option
do
c
ument
a
tio
n
.
.
.
commit
|
commitdiff
|
tree
2012-02-03
D
a
vid van der
S
poel
Merge
"
Improved th
e
accura
c
y
of the sd1 integrator
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
Davi
d
van
d
er S
p
oel
Mer
g
e
"g_s
a
n
s
-
tool to
comput
e
S
ANS sp
e
ctr
a
" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
D
av
i
d va
n
der Spoel
M
e
rge "Fixed erro
r
message to id
e
ntify th
e
c
or
r
ect
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
Da
v
id van d
e
r S
p
oel
Me
r
g
e "F
i
xed trj
c
o
n
v
-sub"
i
nto
r
elease-4-5
-
patches
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
Merg
e
"Improved
e
r
r
or
m
essa
g
e" into releas
e
-4
-
5-patches
commit
|
commitdiff
|
tree
2012-01-31
David van
der Spoel
Merge "Fix
I
C
C on
W
indows Build" into release-4-5-pa
t
ches
commit
|
commitdiff
|
tree
2012-01-31
David van der S
p
oel
Changed order of para
m
eters in top fil
e
commit
|
commitdiff
|
tree
2012-01-25
David van der Spoel
Added
t
wo new bonded functions
.
commit
|
commitdiff
|
tree
2012-01-20
David v
a
n
d
e
r
S
p
oel
Merge "Fixed timing mea
s
u
r
eme
n
ts
.
" into releas
e
-
4
-5
.
.
.
commit
|
commitdiff
|
tree
2012-01-17
David van der
Spoe
l
Repl
a
c
e
s
tderr by
stdout in editconf termin
a
l
o
utput
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
D
a
vid van
der Spoel
Intr
o
d
u
ced fatal err
o
r in grompp
for
in
c
orrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
Commented out part o
f
this new pr
o
gram that was
not
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
Fixed docum
e
nta
t
ion
issue described in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
F
i
x
ed docum
e
ntation is
s
ue described
i
n redmin
e
issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David
van der Spoel
Fixed compilation
i
ss
u
es
commit
|
commitdiff
|
tree
2011-09-19
D
avid van
d
er
S
poel
R
e
solved gerrit issu
e
https://gerrit
.
groma
c
s
.
org/
#
change,126
commit
|
commitdiff
|
tree
2011-09-13
David van der
S
poel
Added
w
arning line
.
commit
|
commitdiff
|
tree
2011-07-20
David van der Spo
e
l
Merge br
a
nch 'release-4-
5
-patches'
o
f g
i
t@g
i
t
.
gro
m
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
Dav
i
d van der
S
p
oel
Added initialization of array
s
a
f
ter srenew c
a
ll
.
commit
|
commitdiff
|
tree
2011-07-01
David v
a
n der Spoel
M
erge
br
a
nch 'release
-
4-5-pa
t
ches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
D
a
vid van
der Spo
e
l
Merge bran
c
h 'rel
e
ase-4-5-patches' of
gi
t
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der
Spoel
Further patches
t
o
fluctuation co
d
e and d
e
nsity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Adde
d
quot
e
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van der S
p
oel
Merge branch 'release-
4
-5-p
a
t
c
hes' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
a
vid va
n
der
S
poel
Merge
b
ranch 'release-4-5-patch
e
s'
of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
Da
v
id va
n
der Spoel
Re-im
p
lemented the
fl
u
ct
u
ation an
a
l
ysis, based on Enthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-07
D
avid
van der Sp
o
el
Added comput
a
t
i
o
n of A
an
d
U
.
commit
|
commitdiff
|
tree
2011-05-06
David van der Spoel
Updated, made default toleran
c
e for
bisec
t
o
r
more
s
tringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
David van der S
p
oel
Fixed weight fu
n
ctions and add
e
d -dump option (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
David van der
S
poel
Upda
t
ed
.
F
i
x
e
d
com
p
utation of
frequency
.
commit
|
commitdiff
|
tree
2011-05-06
Davi
d
v
a
n der Spo
e
l
M
e
rge
b
ranch 'r
e
lease-4-5-pa
t
c
hes' of git
@
g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-02
Dav
i
d van der Spoel
U
p
d
a
t
ed the eqn for c
o
m
p
u
ting Delta
.
Now get roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-01
David van d
e
r Spoel
M
u
lt
i
plied the
D
o
S by t
h
e timestep
(
between fra
m
es)
.
commit
|
commitdiff
|
tree
2011-04-26
David van d
e
r
S
poel
Upd
a
ted
.
N
o
w
computes
d
iffusion from the VACF
.
commit
|
commitdiff
|
tree
2011-04-23
David van de
r
Spoel
Fixed x
-
ax
i
s to be in
r
e
ci
p
rocal
c
m
.
commit
|
commitdiff
|
tree
2011-04-23
David v
a
n
de
r
Spo
e
l
Furth
e
r upda
t
es
.
Still not pe
r
f
ect
.
commit
|
commitdiff
|
tree
2011-04-22
David v
a
n
der
S
poel
A
d
ded stuf
f
to comput
e
cP and S
.
Not complete
y
et
.
commit
|
commitdiff
|
tree
2011-04-21
David van der Sp
o
el
Upda
t
e
d
to
com
p
ute the f
l
uid
i
c
i
t
y
.
Added
refs
f
or citation
.
commit
|
commitdiff
|
tree
2011-04-21
Davi
d
van der
S
poel
First version of a
Densi
t
y of Sta
t
es analysis tool
.
commit
|
commitdiff
|
tree
2011-04-10
David
van der Spoel
Merge branch 'release-
4
-5-pa
t
ch
e
s' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
Da
v
i
d
van der S
p
oel
A
dded g_hydor
d
er
.
1 man
p
age
.
commit
|
commitdiff
|
tree
2011-04-06
David
v
an der Spoel
Fixed h
e
ader for gmx_conect_init
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n der
S
p
o
el
Merge branch 'release-4-5-
p
atches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
v
a
n der Spoel
Removed superf
l
uous file
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
van der S
p
o
e
l
Mad
e
new
programs compile w
i
th gcc -pedanti
c
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
v
a
n de
r
Spoel
New
en
t
r
y
commit
|
commitdiff
|
tree
2011-04-04
D
a
vid van
der Spoel
Added 1 analysi
s
tool manua
l
.
commit
|
commitdiff
|
tree
2011-04-04
David
v
an der S
p
o
e
l
Merge bran
c
h 'releas
e
-4-5
-
pa
t
ches' into orderparm
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n de
r
Spoel
Latest fixes from
Bj
o
rn Steen Sa
e
t
h
re
commit
|
commitdiff
|
tree
2011-03-24
David van der Spoel
A
dded Bjorn's code, imple
m
e
nted running a
v
erage f
i
lterin
g
.
commit
|
commitdiff
|
tree
2011-03-05
David van de
r
Spoel
Merge
b
r
anch 're
l
e
ase-4-5-patc
h
es' of git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David van der Spoe
l
Fixed SE
G
V i
n
eneconv w
h
en
u
s
in
g
t
h
e
-e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David
v
an der Spo
e
l
Fi
x
ed more PBC
a
nd indexing s
t
uff
.
commit
|
commitdiff
|
tree
2011-01-30
David v
a
n der Spoel
F
i
xe
d
typo
.
commit
|
commitdiff
|
tree
2011-01-30
David van der
Spoel
Merge branch
'
release-
4
-
5
-patches' int
o
orderparm
commit
|
commitdiff
|
tree
2011-01-29
David van
d
er Spo
e
l
Mer
g
e br
a
n
c
h
'
release-4-5-patches' of git@g
i
t
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
Davi
d
van der Spoel
Added code in g_
n
me
i
g
to comp
u
te
t
he quantu
m
corr
e
ctions
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David van der
S
poel
M
e
r
g
e
bra
n
ch 'release-4-5-patches' of git@git
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David v
a
n der Spoel
Fixed bug 678 which was
due to
calling
g
m
x_fatal withou
t
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
David van der
Spoel
Merge
b
ranch
'
release-4-5-patches' of git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van der Spoel
A
d
d
ed
w
ar
n
ing in g_dipoles
commit
|
commitdiff
|
tree
2010-12-23
David va
n
der Spoel
Fi
x
ed bug in statistics which di
d
not
all
o
w fitti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David
van d
e
r Sp
o
el
Merg
e
branch 'release-
4
-5-pa
t
ch
e
s' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Da
v
id van der
Spoel
Ad
d
ed 1 qu
o
t
e
.
commit
|
commitdiff
|
tree
2010-12-09
D
avi
d
van der Spoel
Added
f
a
t
al error for
w
hen p
e
ople use energy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
Da
v
id v
a
n de
r
S
p
oel
F
ixed
b
ugzi
l
la 616 a
b
o
u
t formatt
i
ng in t
h
e
help
te
x
t
.
commit
|
commitdiff
|
tree
2010-11-26
David van der Spoe
l
Fixed
S
EGV bug in g_sh
a
m
.
commit
|
commitdiff
|
tree
2010-11-18
David
va
n
de
r
Spo
e
l
Made pr
i
nti
n
g
i
n check_mu
l
ti_init conditiona
l
,
d
e
p
ending
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Dav
i
d van d
e
r Spoel
Fix
e
d bug 60
8
by thr
o
wi
n
g a fat
a
l
err
o
r
in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
David van
d
er Sp
o
el
Merg
e
bran
c
h 'releas
e
-4-5-patches' of
g
it
.
gro
m
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
D
avid
van d
e
r Spoel
Merge branch 'release-4-5-patc
h
es'
o
f git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David van der Spoel
Fixed com
p
ilati
o
n issues with C99 co
m
p
atibility
.
commit
|
commitdiff
|
tree
2010-10-07
D
a
vid va
n
der Spoel
Fi
x
es
a
n
d sm
a
ll
a
dditions to g_wha
m
, due
t
o
Joch
e
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
D
a
vid van
d
e
r
Spoel
Re-add
e
d
g
_
k
inetics to src/tools/M
a
k
e
file
.
am
commit
|
commitdiff
|
tree
2010-09-25
David
va
n
d
er Spoel
A
dded software-related quot
e
commit
|
commitdiff
|
tree
2010-09-24
David van der Spoel
Upda
t
ed to reflect bug
557
.
commit
|
commitdiff
|
tree
2010-09-20
David van der Spoel
Mer
g
e branch 'release-4-
5
-p
a
tch
e
s' o
f
g
i
t@gi
t
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Davi
d
v
a
n
d
er S
p
oel
F
i
xed
b
u
g http://bugzilla
.
gromacs
.
o
r
g/show_b
u
g
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
D
a
vid van
der
S
poel
Co
r
re
c
ted name of one of t
h
e developers li
s
ted in header
.
commit
|
commitdiff
|
tree
2010-09-14
Dav
i
d v
a
n
der S
p
oel
F
ixed bug 553 by checking whether an atom n
a
me is longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David v
a
n der
Spoe
l
Fixed demo to w
o
r
k
wit
h
new pdb2g
m
x that
r
equires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
D
a
vid
van
d
e
r
Spo
e
l
M
ade genre
s
tr -constr t
o
produce constraints of type
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
D
avid van der Spoel
Fixed bug 417
.
commit
|
commitdiff
|
tree
2010-08-19
David van d
e
r Spoel
Fixes more
m
i
sery i
n
function skipstr, where poi
n
t
e
rs
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Dav
i
d van der Spoel
Ad
d
e
d two
m
issing inc
l
ude files
.
Fixed
h
orrible coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Davi
d
van der S
p
oel
Fixed r
e
use of va
r
iable as temp variabl
e
before printin
g
.
.
.
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