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Replace all command line parsing with Options
2014-06-07
T
e
emu Murtola
Re
p
lace all c
o
mmand line parsing
w
ith Options
commit
|
commitdiff
|
tree
2014-06-07
Teemu Mu
r
tola
Move residue
t
y
p
e handling to its own file
.
commit
|
commitdiff
|
tree
2014-06-07
Teem
u
Murt
o
la
Rem
o
ve support for "old" index file forma
t
commit
|
commitdiff
|
tree
2014-05-31
Magnu
s
L
u
ndborg
Fix bu
g
writin
g
TNG output fro
m
dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Bug fix in t
h
e TNG
l
ibrary to improve reading
.
commit
|
commitdiff
|
tree
2014-05-24
Mark
Ab
r
a
ham
Move tools code
to where it is
u
se
d
commit
|
commitdiff
|
tree
2014-05-18
Teemu Mu
r
tola
M
o
ve 3dview
.
* to progra
m
s/view/
commit
|
commitdiff
|
tree
2014-05-16
David van der Spoe
l
Fixe
s
a complic
a
ted bug in g_an
a
eig
.
commit
|
commitdiff
|
tree
2014-03-17
Te
e
mu Mur
t
ola
Update manual
a
nalys
i
s se
c
t
i
o
n
commit
|
commitdiff
|
tree
2014-02-21
N
ina Fischer
Added n
e
w ambe
r
99
s
b-ildn-bs
c
0 force field
.
commit
|
commitdiff
|
tree
2014-02-10
Dav
i
d
van der Spoel
Mov
e
d
conditional cm
a
ke code
f
or vmdio
.
commit
|
commitdiff
|
tree
2014-01-19
Mark Abraham
Clean
up after gmxcp
p
commit
|
commitdiff
|
tree
2013-12-23
David v
a
n der
Sp
o
e
l
Fixed compilation issue due
to
g
cc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
David van der Spoel
Fixes #1312 uninitialized
error
i
n
g_e
n
emat
.
commit
|
commitdiff
|
tree
2013-05-16
David van der Spoel
Fixed two compilation iss
u
e
s
.
commit
|
commitdiff
|
tree
2013-05-02
David van
d
er
Spoel
Fixes #1
2
38 g_hydor
d
er d
o
es no
t
call set_pbc
.
commit
|
commitdiff
|
tree
2013-03-07
David van
der Spoel
Fixe
s
#118
3
PBC bug i
n
g
_
m
i
ndis
t
commit
|
commitdiff
|
tree
2013-02-13
D
avid van der
Spoel
Plain t
e
xt quotes
.
commit
|
commitdiff
|
tree
2012-11-26
David van der
S
poel
Fi
x
es #10
3
5 NaN in g_cluster
o
u
tput
.
commit
|
commitdiff
|
tree
2012-11-20
D
a
vid van d
e
r
S
poe
l
Fixes bu
g
in
g_hbond
that makes it produce fatal
err
o
r
.
commit
|
commitdiff
|
tree
2012-10-21
D
a
vid van der Spoel
F
i
x
e
d Bu
g
#593 about memory ho
l
e
in tr
j
cat
.
commit
|
commitdiff
|
tree
2012-10-04
David van der Spo
e
l
Set
ret
u
rn value to FALSE
(
0
)
in
e
s
timat
e
_dt in lib
x
d
r
f
.
c
commit
|
commitdiff
|
tree
2012-09-07
David van der Spoel
Adapted NMR
r
ela
t
ed data to n
e
w pdb f
o
rma
t
.
commit
|
commitdiff
|
tree
2012-09-04
David van der Spoel
M
a
de tutorial
s
l
i
ghtly less confusing
.
commit
|
commitdiff
|
tree
2012-08-16
David
v
an de
r
Spoel
Optional computation o
f
fluct
.
p
r
op
s
in g_en
e
rgy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
D
avid van der
Spoel
Fixed bug in free
energy calcul
a
ti
o
n for M
o
rse pote
n
ti
a
ls
commit
|
commitdiff
|
tree
2012-06-21
Da
v
i
d
van der
S
po
e
l
Fixes #
9
61 - Shake re
p
or
t
s
w
rong
e
r
ror
commit
|
commitdiff
|
tree
2012-03-17
David van der Spoel
Removed qhop
f
iles f
r
om this branch
.
commit
|
commitdiff
|
tree
2012-03-10
D
avid van der Spo
e
l
V
i
b
r
a
tion spectra from vel
o
city A
C
F or Normal modes
.
commit
|
commitdiff
|
tree
2012-01-31
David van der Sp
o
e
l
Changed order of par
a
m
e
t
e
rs in top file
commit
|
commitdiff
|
tree
2012-01-25
D
avid van der Spoel
Added two new bonded functi
o
ns
.
commit
|
commitdiff
|
tree
2012-01-17
Davi
d
van der Spoel
Replace stderr by stdout in editconf terminal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
D
a
vid va
n
d
e
r
Spoel
In
t
roduced fatal error in grompp f
o
r i
n
correct
use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Davi
d
van der Spoel
C
o
mmented out part
o
f th
i
s
n
ew program
t
h
at was not
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
avid van der Spoel
Fixed document
a
tion is
s
ue described i
n
redm
i
ne iss
u
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
a
vid va
n
der Spoel
Fixed docum
e
nta
t
i
on issue desc
r
ibed in redmine issu
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Dav
i
d
van d
e
r
Spoel
Fixed comp
i
lati
o
n iss
u
e
s
commit
|
commitdiff
|
tree
2011-09-19
D
avid
van der Spoel
Res
o
lved gerrit issu
e
https://gerrit
.
gromacs
.
org/
#
c
h
a
nge,126
commit
|
commitdiff
|
tree
2011-09-13
D
a
vid
van der Spoel
Added
w
ar
n
ing li
n
e
.
commit
|
commitdiff
|
tree
2011-07-20
Davi
d
van der
Sp
o
e
l
Mer
g
e
b
r
anch 'rel
e
a
s
e
-
4-5-patc
h
es' of git@git
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
David van der S
p
oel
Added init
i
alization
of
a
rray
s
a
f
ter srenew call
.
commit
|
commitdiff
|
tree
2011-07-20
Davi
d
van
d
er
Sp
o
el
Ad
d
e
d
in
i
t
i
ali
z
ation
o
f
arr
a
ys after srenew call
.
commit
|
commitdiff
|
tree
2011-07-02
Da
v
id van der Spoel
Merge
branch
'master' of
git
@
git
.
g
r
o
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2011-07-02
David v
a
n der Spoel
C
o
mpilation fix
e
s
in
gmx_density
.
c and histogram
.
cp
p
commit
|
commitdiff
|
tree
2011-07-01
David
van d
e
r Spoel
M
e
rge
branch 'release-4-5-pat
c
hes' of git@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Dav
i
d v
a
n der Spoel
Merg
e
b
r
anch '
r
ele
a
se-4-5
-
patche
s
' o
f
git@git
.
g
ro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der Spo
e
l
A
d
d
e
d
g
_dos tar
g
et
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d v
a
n
d
er
S
poel
F
u
rther patches
t
o fluctuation code
a
nd d
e
n
s
ity o
f
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
d
er Sp
o
el
Add
e
d compu
t
ation of A and
U
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
v
an der Spoel
Updated, made d
e
fault to
l
erance for
b
i
s
ector more stringe
n
t
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
v
a
n
der Spoe
l
F
ixed weigh
t
functions and a
d
ded -
d
ump option (h
i
dden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David
van der Spoe
l
Updated
.
Fixed compu
t
a
tion of frequen
c
y
.
commit
|
commitdiff
|
tree
2011-05-31
David
va
n
der Spoel
U
p
dated th
e
e
q
n for computin
g
Delta
.
Now get roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Multipl
i
ed
t
he DoS by
the
t
imestep (b
e
tween frames)
.
commit
|
commitdiff
|
tree
2011-05-31
D
avid van der Spoel
Updated
.
Now computes d
i
ffu
s
i
on
f
rom the VACF
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
an der
Spo
e
l
F
i
xed x-axis
t
o be in reciprocal cm
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
an der
S
poel
Furth
e
r
updates
.
Still not perfect
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
v
id van d
e
r Spoel
Added stuf
f
t
o
comput
e
c
P
and S
.
N
o
t complete yet
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
an der Spoe
l
Updated to compute the fluidicity
.
Added ref
s
for citation
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r
S
poel
Update
d
commit
|
commitdiff
|
tree
2011-05-31
David
v
an
d
er Spoel
New
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id van
de
r
Spoel
Further
p
atc
h
e
s
to fluct
u
ation code and
d
ens
i
ty
o
f
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spo
e
l
M
e
rge branch
'master' of git@git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2011-05-31
David
v
an de
r
S
poel
A
d
ded quote
.
commit
|
commitdiff
|
tree
2011-05-31
David v
a
n der Spoel
Further patches
to fluc
t
uatio
n
code and densit
y
of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
avi
d
van d
e
r Spoel
Added
quote
.
commit
|
commitdiff
|
tree
2011-05-31
D
avi
d
van der Spoel
Merge branch 'rele
a
se
-
4-5-patches' of
g
i
t
@git
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David v
a
n d
e
r Spoel
Merge branch 'release-4-
5
-p
a
tches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van der Spoel
Re-i
m
p
l
emented the fluc
t
uation anal
y
sis,
based on
Enthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
a
v
i
d va
n
d
e
r
Spoel
Re
-
im
p
le
m
en
t
ed the f
l
uctuatio
n
analys
i
s,
b
ased on Ent
h
alpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-07
Davi
d
van der Spoel
Added computation of A an
d
U
.
commit
|
commitdiff
|
tree
2011-05-06
Dav
i
d van
d
er Spoel
Upda
t
e
d
, made defaul
t
tolerance for
b
isector more s
t
r
ingen
t
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
D
avid van der
Spoel
Fixed
w
eight functions and added -dump option (hi
d
de
n
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
vid van der
Spoel
Updated
.
Fixed computation of frequency
.
commit
|
commitdiff
|
tree
2011-05-06
Da
v
i
d van der Spoe
l
M
erge b
r
anch 'releas
e
-4-5-
p
atch
e
s
'
o
f
git
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-02
Dav
i
d van
der Spoel
Up
d
ated the
e
qn
f
or computi
n
g Delta
.
Now get
roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-01
David van der Sp
o
el
Mul
t
ipli
e
d the
DoS
by th
e
timestep
(be
t
w
e
en frames)
.
commit
|
commitdiff
|
tree
2011-04-26
Dav
i
d v
a
n
der Spoel
Updated
.
Now
c
om
p
u
tes diffusion from t
h
e
VACF
.
commit
|
commitdiff
|
tree
2011-04-23
David van de
r
Spoel
Fix
e
d x-ax
i
s to be in reci
p
rocal cm
.
commit
|
commitdiff
|
tree
2011-04-23
David v
a
n der S
p
oel
Fu
r
ther updates
.
Still
no
t
perfect
.
commit
|
commitdiff
|
tree
2011-04-22
David va
n
der Spo
e
l
Added stuf
f
to compute
cP and S
.
N
o
t comp
l
e
t
e yet
.
commit
|
commitdiff
|
tree
2011-04-21
David van der Sp
o
el
U
p
dated to compute the fl
u
i
di
c
ity
.
Added refs for citation
.
commit
|
commitdiff
|
tree
2011-04-21
D
avid van der S
p
oel
Fi
r
s
t versio
n
of a Density of States analysis tool
.
commit
|
commitdiff
|
tree
2011-04-10
David van
der S
p
oel
M
e
rge
b
ranc
h
'release-
4
-5-patches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
David van der Spoel
Added g_hydorder
.
1
man
page
.
commit
|
commitdiff
|
tree
2011-04-06
Davi
d
van
der Spo
e
l
F
i
x
ed h
e
ader
f
or gmx_conect_init
commit
|
commitdiff
|
tree
2011-04-06
David van der Spoel
Fixe
d
header for
gmx_con
e
ct_init
commit
|
commitdiff
|
tree
2011-04-04
David van der Spo
e
l
Merge branch 'release-4-5-pa
t
ches' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
David van der Sp
o
el
Removed su
p
erfluous
file
.
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
Mad
e
new program
s
compile with
gcc -pedantic
.
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
New entry
commit
|
commitdiff
|
tree
2011-04-04
D
avi
d
va
n
d
e
r Spoe
l
Add
e
d
1
analysis tool
m
a
nual
.
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
Merge branch 'rele
a
s
e
-4-5-
p
atches' i
n
to or
d
erparm
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n d
e
r Spoel
L
atest fi
x
es from Bjo
r
n S
t
e
e
n
Saethre
commit
|
commitdiff
|
tree
2011-03-24
David van der Spoel
Added
B
jo
r
n's code, impl
e
m
ented runnin
g
average filtering
.
commit
|
commitdiff
|
tree
2011-03-05
D
a
vid van der Spoel
Merge branch 'release-4-5-patches'
o
f
gi
t
@g
i
t
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David
van der Spoel
Fix
e
d SEGV in enec
o
nv when using the -e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David
van der S
p
oe
l
Fixed more PBC and index
i
ng stuff
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
F
ixe
d
t
y
p
o
.
commit
|
commitdiff
|
tree
2011-01-30
D
a
vid van
der S
p
o
el
Merge branch
'
r
e
lease
-
4-5-p
a
tches' into orderp
a
r
m
commit
|
commitdiff
|
tree
next