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Removed types/mdatom.h from typedefs.h
2015-09-30
David van der Spoel
Remove
d
types/mdatom
.
h f
r
om type
d
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
van der Spoel
Remove
d
t
ype
s
/inp
u
trec
.
h
from typedefs
.
h and
r
eleted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Mark Abraham
C
l
ean u
p
of tab
l
es
c
o
de
commit
|
commitdiff
|
tree
2015-09-29
Mark
Abraham
Move
tabl
e
s
.
c
to ne
w
mod
u
le and C++
commit
|
commitdiff
|
tree
2015-09-22
David v
a
n der Spo
e
l
Removed four
i
n
c
l
u
des from leg
a
cyheaders/typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Dav
i
d van
d
e
r Spoel
Rem
o
ved legacyheaders/types/commrec_fwd
.
h
f
rom typed
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van de
r
S
p
oe
l
Removed
<
sys/types
.
h
>
a
nd
"
types/
c
onstr
.
h" f
r
om typedefs
commit
|
commitdiff
|
tree
2015-09-08
David
van d
e
r S
p
oel
M
oved functions ope
r
ating
o
n for
c
erec to separ
a
t
e
header
.
commit
|
commitdiff
|
tree
2015-09-04
Rossen
A
p
o
stolov
Converted
e
ssentialdynamic
s
module to C+
+
.
commit
|
commitdiff
|
tree
2015-08-03
David va
n
d
er
S
po
e
l
Made output from dumpin
g
neight
b
orlists easie
r
to
re
a
d
.
commit
|
commitdiff
|
tree
2015-07-29
Erik Lindahl
Moved
a
n
o
ther bun
c
h
of mdlib
u
tils to
C
++
commit
|
commitdiff
|
tree
2015-07-29
E
r
i
k
Lin
d
ahl
Up
d
a
t
e
namin
g
st
a
n
d
ards to avo
i
d h
u
ngarian notation
.
.
.
commit
|
commitdiff
|
tree
2015-07-24
Teemu Murtola
Rename trnio
.
* to trrio
.
*
commit
|
commitdiff
|
tree
2015-05-12
Jo
c
he
n
Hu
b
OpenMP parallelization of g_wham
commit
|
commitdiff
|
tree
2015-04-09
David
v
an
d
e
r Sp
o
el
Clarifie
d
comments for time-depen
d
ent electric fie
l
ds
.
commit
|
commitdiff
|
tree
2015-04-08
David van
d
er Spo
e
l
F
i
xed inc
o
rrect out
p
ut of gb_al
g
orith as sa_algorithm
.
commit
|
commitdiff
|
tree
2014-10-28
Davi
d
van der Spoel
Even
m
o
r
e refreshin
g
quot
e
s
.
commit
|
commitdiff
|
tree
2014-09-22
M
ar
k
Abraham
More quotes
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
More quot
e
s
commit
|
commitdiff
|
tree
2014-09-19
Teem
u
Mu
r
tola
Add sup
p
ort for cumulative
histogram
s
commit
|
commitdiff
|
tree
2014-09-17
David van der Spoel
Merge re
l
ease-5-0 into master
commit
|
commitdiff
|
tree
2014-08-30
Dav
i
d
v
an
d
e
r
Spoel
Fixes issu
e
with vsite
n
a
nd v
e
rl
e
t buffers
.
commit
|
commitdiff
|
tree
2014-06-25
David
va
n
der Spoel
A
d
ded check fo
r
domain decomposition
a
nd shells
.
commit
|
commitdiff
|
tree
2014-06-22
David va
n
der Spoel
Implement
e
d fatal
e
rror
for nstcal
c
en
e
rgy!=1
with shells
.
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Made shell
s
work with the Verle
t
scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk He
s
s
Made
g
m
xcheck -
r
m
sd
w
o
r
k
a
gain w
i
th fo
r
ces
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Make
s
ure genrestr uses the disre_up2 parameter
commit
|
commitdiff
|
tree
2014-06-12
Erik Li
n
dahl
R
e
moved undo
c
umente
d
-
m
ap and
-
m
data options f
r
om g_sham
.
commit
|
commitdiff
|
tree
2014-06-12
Eri
k
Linda
h
l
Always write
o
u
tput fro
m
genion
commit
|
commitdiff
|
tree
2014-06-11
David van der Spoel
Fixes bug where -e and -dt flags did not work an
y
more
.
commit
|
commitdiff
|
tree
2014-06-11
B
erk Hess
M
a
de repl_ex time step more readable
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtola
Impro
v
e
(Selection|File
N
ame)Opt
i
onManager hand
l
in
g
commit
|
commitdiff
|
tree
2014-06-07
T
e
e
mu Murtola
Replace all
c
ommand line parsing
w
i
th O
p
tions
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtola
Move residuetype handl
i
ng to its own file
.
commit
|
commitdiff
|
tree
2014-06-07
T
e
emu Murtola
Remove suppor
t
for "old" index file format
commit
|
commitdiff
|
tree
2014-05-31
M
agnus
L
undborg
Fix
bug wr
i
ting TNG out
p
ut from
dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lun
d
borg
Bug fix in the TNG
l
ibrary to improve readi
n
g
.
commit
|
commitdiff
|
tree
2014-05-24
Mark Abraham
Mo
v
e tools co
d
e to where it is
used
commit
|
commitdiff
|
tree
2014-05-18
Tee
m
u Murto
l
a
Move 3dview
.
* to progr
a
ms/view/
commit
|
commitdiff
|
tree
2014-05-16
D
avid v
a
n der Spoel
Fixe
s
a
complicated bug in
g
_anaei
g
.
commit
|
commitdiff
|
tree
2014-03-17
Tee
m
u Murtola
Update manual analysis section
commit
|
commitdiff
|
tree
2014-02-21
Ni
n
a Fischer
Ad
d
ed new ambe
r
9
9sb
-
ildn-bs
c
0
force field
.
commit
|
commitdiff
|
tree
2014-02-10
Davi
d
v
an der
S
poel
M
o
ved conditional cmake co
d
e for
v
m
dio
.
commit
|
commitdiff
|
tree
2014-01-19
Mark Abraha
m
C
l
ean up a
f
ter
g
mxcpp
commit
|
commitdiff
|
tree
2013-12-23
David van der Spoe
l
F
i
xed comp
i
lation i
s
sue due to gcc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
Da
v
i
d van de
r
S
p
oel
Fixes
#1312 uninitialized error in
g_enemat
.
commit
|
commitdiff
|
tree
2013-05-16
Dav
i
d van der Spoe
l
Fixed two
compilation issues
.
commit
|
commitdiff
|
tree
2013-05-02
Dav
i
d van der Spoel
Fixes #1
2
3
8
g_hydord
e
r
d
oes not call
s
et_pbc
.
commit
|
commitdiff
|
tree
2013-03-07
David van der Sp
o
el
Fixes #11
8
3 PB
C
b
ug in g_mindist
commit
|
commitdiff
|
tree
2013-02-13
David v
a
n der Sp
o
el
Plain
text quot
e
s
.
commit
|
commitdiff
|
tree
2012-11-26
Da
v
id va
n
der Spoel
F
i
xes #1035
N
aN in g_cluster output
.
commit
|
commitdiff
|
tree
2012-11-20
D
avi
d
van der
S
p
o
el
Fixes bu
g
i
n g_hbond that
m
akes it produce fatal err
o
r
.
commit
|
commitdiff
|
tree
2012-10-21
David va
n
der
S
p
oel
Fixed
Bug #593
about memory hole in
trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
David va
n
der
S
poe
l
Set re
t
urn
value to FAL
S
E
(0)
in e
s
timate_
d
t in libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-07
Da
v
i
d van der Spoel
Adapted NMR rel
a
ted da
t
a
t
o ne
w
pdb for
m
at
.
commit
|
commitdiff
|
tree
2012-09-04
David
van der Spo
e
l
Made tut
o
r
ial s
l
i
ghtly less
c
onfus
i
ng
.
commit
|
commitdiff
|
tree
2012-08-16
David
v
an der Spo
e
l
Opt
i
onal com
p
u
tation of fluc
t
.
props in g_energy
.
Fi
x
es
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
Davi
d
v
an der Spoel
Fixe
d
bug in free
e
nergy
calculation for
M
o
r
s
e potentials
commit
|
commitdiff
|
tree
2012-06-21
D
avi
d
van der Spoel
Fixes #961 - Shake re
p
orts wrong er
r
or
commit
|
commitdiff
|
tree
2012-03-17
D
avid
v
an der S
p
oe
l
Removed qhop files from
t
his
b
r
a
n
c
h
.
commit
|
commitdiff
|
tree
2012-03-10
David
v
an der Spoe
l
V
ibration
spectra from veloc
i
ty A
C
F or Normal mo
d
es
.
commit
|
commitdiff
|
tree
2012-01-31
David van der Spoel
Changed orde
r
of paramete
r
s in top file
commit
|
commitdiff
|
tree
2012-01-25
David van der Spoel
Added two new bonded funct
i
on
s
.
commit
|
commitdiff
|
tree
2012-01-17
David van der S
p
oel
Repla
c
e
stderr
b
y
stdo
u
t
in e
d
itconf ter
m
inal ou
t
put
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David van
der Spoel
I
ntroduced fatal error
in g
r
omp
p
f
or incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
av
i
d
van de
r
Spoel
Commente
d
out part of this new program that was
n
ot
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
a
vid van
d
er
Spoel
Fixed document
a
tion issu
e
described
i
n red
m
ine iss
u
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David
van der Spo
e
l
Fixed
documenta
t
ion
i
ssue des
c
rib
e
d
i
n redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David van der Spoel
Fixed compilat
i
on issues
commit
|
commitdiff
|
tree
2011-09-19
David v
a
n der
S
poel
Resolved gerrit issue ht
t
ps:/
/
ger
r
it
.
gromac
s
.
org/#change
,
126
commit
|
commitdiff
|
tree
2011-09-13
David van de
r
S
p
oel
A
d
d
ed warning line
.
commit
|
commitdiff
|
tree
2011-07-20
D
a
vid van de
r
Spoel
M
e
rge branch 'rel
e
ase
-
4
-
5-pat
c
hes'
of git@git
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
David van
d
er S
p
oe
l
Added
init
i
alizati
o
n of arrays
a
fter sre
n
ew c
a
ll
.
commit
|
commitdiff
|
tree
2011-07-20
David van der
S
poel
Added initiali
z
ation
o
f arrays after
s
renew call
.
commit
|
commitdiff
|
tree
2011-07-02
D
a
vid van
der Sp
o
el
M
erge
b
ranch 'mast
e
r' of
git@git
.
gromacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2011-07-02
David van der Spoel
Com
p
il
a
tion fixes in gmx_den
s
ity
.
c a
n
d
his
t
ogram
.
cpp
commit
|
commitdiff
|
tree
2011-07-01
Da
v
id
v
an
de
r
Spo
e
l
M
e
rge branch 'relea
s
e-
4
-5-patch
e
s' of git@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Dav
i
d van der Spoel
M
erge branc
h
'r
e
lease-4-
5
-
p
at
c
hes'
o
f git
@
git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Davi
d
van der Spo
e
l
Added
g_
d
o
s target
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id
v
an der Spoel
Further patches to fluct
u
ation code and density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van
d
er Spoe
l
Added com
p
utat
i
on
o
f
A and
U
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der Spoel
U
pdated, made de
f
ault tolerance for bisecto
r
m
ore stringe
n
t
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Fixed weigh
t
functions and add
e
d -dump o
p
tion (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
Updated
.
Fixed c
o
m
p
utat
i
on
o
f frequency
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id va
n
der
S
poel
Updated the eqn
for c
o
mputing De
l
ta
.
Now get roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David
van d
e
r Spo
e
l
Multiplied the DoS by
the
ti
m
estep (b
e
twe
e
n frames)
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Updated
.
Now
c
omputes
d
iffusion from the VACF
.
commit
|
commitdiff
|
tree
2011-05-31
David van
der
S
poel
Fixed x-axis
to
be in reciprocal cm
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id va
n
der
S
poel
Further
updates
.
S
t
i
l
l not perfect
.
commit
|
commitdiff
|
tree
2011-05-31
David
van der Spoe
l
Ad
d
e
d
st
u
ff to
c
ompute cP
an
d
S
.
N
o
t complete yet
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
Updated to compute the fluidicity
.
Add
e
d re
f
s f
o
r ci
t
ation
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
der Spoel
Updated
commit
|
commitdiff
|
tree
2011-05-31
David van der Spo
e
l
New
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van der
S
poel
Furth
e
r patches to f
l
u
ctuatio
n
code an
d
d
e
nsity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van
d
er Spo
e
l
Merge branch 'master' o
f
git@git
.
g
romacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
v
a
n der Spoel
Added
q
uote
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van
der Spoel
Further patches to flu
c
tuation
c
ode and density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David v
a
n der Spoel
Added quote
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid v
a
n der Spoe
l
Me
r
ge bran
c
h '
r
elease-4-5-patches' o
f
g
it@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
a
vid
van der Spoel
Merge branch '
r
elease-4-5-patches' of git@git
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
next