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Fix small leaks in do_md cleanup
2015-11-20
D
avid
v
a
n
de
r
Spoel
M
o
ved mdat
o
m
.
h
from legacyhe
a
der/types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van der Spoel
M
erged
l
ega
c
yheaders/
t
ypes/state
.
h into mdtypes
/
state
.
h
commit
|
commitdiff
|
tree
2015-11-14
Berk
Hess
Optimized the bonde
d
thread
f
orce reducti
o
n
commit
|
commitdiff
|
tree
2015-11-13
D
a
vid
va
n
der
S
poel
M
o
ved genborn
.
h to m
d
l
i
b
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved txtdump
.
*
to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Spo
e
l
Moved copyrite
.
* to fil
e
io from gmxlib
and legacyhea
d
ers
.
commit
|
commitdiff
|
tree
2015-10-18
Dav
i
d
v
a
n der
Spoel
Mov
e
d pb
c
/cut-
o
ff related u
t
ilities from typede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
a
vid van der Spoel
Freed
m
emo
r
y in legacy statist
i
cs routi
n
es
.
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
F
i
xed nbnxn
_
4xN
p
e
r
f
o
rmance regr
e
ssio
n
commit
|
commitdiff
|
tree
2015-10-07
B
e
rk Hess
Fix
bugs
with intermol interaction
s
and DD
commit
|
commitdiff
|
tree
2015-10-03
David van der Spoel
R
e
moved
simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spo
e
l
Removed sim
p
le
.
h
from nb_ker
n
el_avx
_
256_XX
commit
|
commitdiff
|
tree
2015-10-01
Teemu Murtola
En
a
ble
time u
n
it and sel
e
c
t
ions i
n
ICommandLineOptionsModul
e
commit
|
commitdiff
|
tree
2015-09-30
David van der
S
poel
R
e
moved types/nbl
i
st
.
h and types/nsgrid
.
h from typ
e
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
v
id
v
a
n der Spoel
Rem
o
ved types/mdat
o
m
.
h from typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David
van der Spoel
Removed
types/in
p
utrec
.
h fr
o
m typedefs
.
h and r
e
leted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Mark Ab
r
ah
a
m
Clean up o
f
t
ables
co
d
e
commit
|
commitdiff
|
tree
2015-09-29
Mark A
b
raham
Move tables
.
c to new module and C++
commit
|
commitdiff
|
tree
2015-09-29
David van der Spo
e
l
Fixes b
u
g i
n
the
comput
a
t
i
on of Coefficie
n
t of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-22
D
avid van der Spoel
Removed fou
r
includes from le
g
acy
h
eaders
/
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David
van d
e
r Spoel
Re
m
oved le
g
acyheader
s
/types/co
m
mrec_fwd
.
h
fro
m
typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
van
d
er Spoel
Remove
d
<sys/types
.
h> and "types/constr
.
h" from typed
e
fs
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
van der Spoel
Moved functions operating on force
r
ec to separate header
.
commit
|
commitdiff
|
tree
2015-09-04
R
ossen Apos
t
olov
Converted essentialdy
n
amics module t
o
C++
.
commit
|
commitdiff
|
tree
2015-09-02
Béla Voß
Avo
i
d integer ove
r
f
l
o
w
in g
m
x_wham by us
i
ng gmx_i
n
t
6
4_t
.
commit
|
commitdiff
|
tree
2015-08-03
Davi
d
v
a
n
d
er Spoel
Made output from dum
p
i
ng ne
i
gh
t
borl
i
sts easier to re
a
d
.
commit
|
commitdiff
|
tree
2015-07-29
Erik Lindahl
Moved another bunch o
f
m
dlib u
t
ils t
o
C
++
commit
|
commitdiff
|
tree
2015-07-29
Er
i
k Lindahl
U
p
date n
a
ming standards to
a
void hungarian
n
otation
.
.
.
commit
|
commitdiff
|
tree
2015-07-24
Teemu Murtola
Rename trnio
.
*
to trrio
.
*
commit
|
commitdiff
|
tree
2015-05-12
Jochen Hub
OpenMP parallelizati
o
n of g_wham
commit
|
commitdiff
|
tree
2015-04-09
David
van der
S
poel
Clarifie
d
c
omment
s
for
t
i
me-depe
n
d
ent elec
t
ric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van der
S
p
oel
F
i
xed incorrect output of gb
_
a
l
gorith
a
s sa_algorit
h
m
.
commit
|
commitdiff
|
tree
2014-10-28
Davi
d
van de
r
S
p
oel
E
v
e
n more refreshi
n
g quot
e
s
.
commit
|
commitdiff
|
tree
2014-09-22
M
a
rk Abraham
Mor
e
qu
o
tes
commit
|
commitdiff
|
tree
2014-09-22
E
rik Lindahl
M
ore
quotes
commit
|
commitdiff
|
tree
2014-09-19
Te
e
mu
Murtola
Add support
for c
u
m
u
lative
h
ist
o
g
r
ams
commit
|
commitdiff
|
tree
2014-09-17
Dav
i
d
van d
e
r Spoel
Merge release-
5
-0 int
o
master
commit
|
commitdiff
|
tree
2014-08-30
Da
v
id van der Spoel
Fixes issue with
v
siten
a
nd verl
e
t
buffers
.
commit
|
commitdiff
|
tree
2014-06-25
D
avid van der
Spoel
A
d
ded chec
k
fo
r
domain decomposition and
s
hells
.
commit
|
commitdiff
|
tree
2014-06-22
David v
a
n d
e
r Spoel
I
mplemented fat
a
l error for nst
c
alce
n
ergy!=1 with shell
s
.
commit
|
commitdiff
|
tree
2014-06-13
Be
r
k Hess
Ma
d
e shells wo
r
k w
i
th the Verle
t
scheme
commit
|
commitdiff
|
tree
2014-06-12
B
erk Hess
M
ade gmxch
e
ck -rmsd
work
again with f
o
rces
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindah
l
Ma
k
e sure genrestr uses the disre_up2 pa
r
amet
e
r
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Rem
o
v
e
d undoc
u
mente
d
-m
a
p and -
m
data
options
f
rom g_sham
.
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
A
l
ways writ
e
ou
t
put fr
o
m
genion
commit
|
commitdiff
|
tree
2014-06-11
David van der Spoel
Fixes bug where
-e and -dt flags did
n
ot work anymore
.
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Made repl_ex
time step m
o
re rea
d
ab
l
e
commit
|
commitdiff
|
tree
2014-06-07
Tee
m
u Murtola
Improve (Select
i
on|F
i
leNa
m
e)Op
t
ionManager handling
commit
|
commitdiff
|
tree
2014-06-07
Teemu M
u
rt
o
la
Replace all comman
d
line pars
i
ng with
Options
commit
|
commitdiff
|
tree
2014-06-07
Teemu M
u
rtola
Move resi
d
u
e
typ
e
han
d
ling to
its ow
n
file
.
commit
|
commitdiff
|
tree
2014-06-07
T
e
emu Murtola
Remove support for "old" ind
e
x f
i
le
f
ormat
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lu
n
d
b
org
Fix bug w
r
iting TNG output from dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundbor
g
Bug
fix in th
e
TNG li
b
rary
to improve
re
a
ding
.
commit
|
commitdiff
|
tree
2014-05-24
Mark Ab
r
aham
Move tools code to wh
e
re it
i
s used
commit
|
commitdiff
|
tree
2014-05-18
Teemu Murtola
M
ove 3dvie
w
.
* to programs/vie
w
/
commit
|
commitdiff
|
tree
2014-05-16
Da
v
id
van der Spoel
Fixes a complic
a
ted bug in g_ana
e
ig
.
commit
|
commitdiff
|
tree
2014-03-17
Teem
u
Murtola
Update man
u
al analysis section
commit
|
commitdiff
|
tree
2014-02-21
N
i
n
a F
i
scher
Added ne
w
amber99
s
b-ildn-bsc0 force fie
l
d
.
commit
|
commitdiff
|
tree
2014-02-10
David
van de
r
Sp
o
el
M
o
v
e
d conditiona
l
cma
k
e
c
ode for vmdio
.
commit
|
commitdiff
|
tree
2014-01-19
M
ark Abraham
Clea
n
u
p
after gmxcpp
commit
|
commitdiff
|
tree
2013-12-23
David
v
an der Spoel
Fixed compilation issue d
u
e to g
c
c4
.
8
commit
|
commitdiff
|
tree
2013-07-24
David
v
an der Spoel
F
ixes #1312 u
n
i
n
itialized error in
g
_
enemat
.
commit
|
commitdiff
|
tree
2013-05-16
David van d
e
r Spoel
F
i
xed two
c
ompilation issues
.
commit
|
commitdiff
|
tree
2013-05-02
D
avid van der
Spoel
Fixes #1238 g_hydorder does not
c
all set_pb
c
.
commit
|
commitdiff
|
tree
2013-03-07
David va
n
der Spo
e
l
Fixes #1183 PB
C
b
ug in g_mindist
commit
|
commitdiff
|
tree
2013-02-13
D
avid van der Spoel
P
l
ain text quo
t
es
.
commit
|
commitdiff
|
tree
2012-11-26
David van der
Spoel
Fixes #1035
NaN
in g_cl
u
s
ter output
.
commit
|
commitdiff
|
tree
2012-11-20
David van de
r
S
poe
l
Fixes bu
g
in g_hbond that makes it produce f
a
tal e
r
ror
.
commit
|
commitdiff
|
tree
2012-10-21
David
van der
S
poel
Fix
e
d
B
ug #593
a
bout mem
o
ry hole
in
trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
David van der Spoel
Se
t
retur
n
v
alue
t
o FAL
S
E (0)
in
e
stimate_dt in libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-07
Dav
i
d
van der
S
poel
Adap
t
ed
NMR
r
elated
data t
o
new pdb format
.
commit
|
commitdiff
|
tree
2012-09-04
David van der Spoel
Made
t
utorial
s
lightly less
c
onfusing
.
commit
|
commitdiff
|
tree
2012-08-16
David van der Spoel
Opt
i
o
nal computation of fluct
.
props in
g
_en
e
rgy
.
F
i
x
es
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
David
van der Spoel
Fixed
b
ug
i
n free energy
c
alculation for Mo
r
se p
o
t
e
nti
a
ls
commit
|
commitdiff
|
tree
2012-06-21
D
avid van der Spoel
Fixes #961 - Sha
k
e reports wr
o
ng erro
r
commit
|
commitdiff
|
tree
2012-03-17
Da
v
i
d va
n
de
r
S
p
oel
Remo
v
ed q
h
op files from this br
a
nch
.
commit
|
commitdiff
|
tree
2012-03-10
David van
de
r
Spoel
Vibration s
p
ectra
f
rom velocity A
C
F or
N
orm
a
l
m
odes
.
commit
|
commitdiff
|
tree
2012-01-31
Dav
i
d van
d
er Spoel
Changed order of parameters in top file
commit
|
commitdiff
|
tree
2012-01-25
David
v
an der Spoel
A
d
ded t
w
o new bo
n
ded functi
o
n
s
.
commit
|
commitdiff
|
tree
2012-01-17
David van
d
er Spoel
Replace
s
tderr by stdout in editconf terminal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David v
a
n der Spoe
l
Int
r
odu
c
ed fat
a
l error
i
n g
r
ompp for
i
n
corr
e
ct use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Da
v
id van der S
p
oel
Commented out part of
t
his
new pro
g
ram that w
a
s no
t
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der
S
poel
Fixed do
c
umentation issue described in r
e
dmine
is
s
ue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van
der Spoel
Fixe
d
document
a
tion
i
s
s
ue
d
e
s
cribed in redmine i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David van der Spoel
Fixed compilation iss
u
es
commit
|
commitdiff
|
tree
2011-09-19
David van der Spoel
R
e
solved
gerr
i
t
is
s
ue https:/
/
ger
r
it
.
g
romacs
.
org/#change,126
commit
|
commitdiff
|
tree
2011-09-13
David van
d
e
r Spoel
A
d
ded warning lin
e
.
commit
|
commitdiff
|
tree
2011-07-20
David va
n
der Spoel
Merge branch 'release
-
4
-
5-
p
atches' of g
i
t@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
David van der Spoel
Added initialization
of ar
r
ays
after srenew call
.
commit
|
commitdiff
|
tree
2011-07-20
David van der
Spoel
Added
initia
l
iza
t
io
n
of arrays after sre
n
ew call
.
commit
|
commitdiff
|
tree
2011-07-02
Da
v
id van
d
e
r
Spoel
Merge b
r
anch 'master' of git@g
i
t
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2011-07-02
David
v
a
n de
r
Spoel
Comp
i
lati
o
n fix
e
s in gmx_density
.
c and histogram
.
cpp
commit
|
commitdiff
|
tree
2011-07-01
David van der Sp
o
el
M
erge branch
'release-4-5-
p
atches' of git@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van
der Sp
o
el
Me
r
ge br
a
n
c
h 'release-4-5-patches' o
f
g
it@git
.
gro
m
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Dav
i
d
v
a
n
der S
p
o
e
l
Add
e
d g_dos targ
e
t
.
commit
|
commitdiff
|
tree
2011-05-31
David van
d
er Spoe
l
F
u
rther patc
h
e
s
t
o
fluctu
a
tion code and densi
t
y of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Added computat
i
on of A and U
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vi
d
v
an der Spo
e
l
U
p
dated, made
default tol
e
rance for bise
c
tor more stringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Sp
o
el
Fixed weight
f
unctio
n
s and added
-dump option
(
h
i
dden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van de
r
S
poel
Updated
.
Fixe
d
co
m
putation o
f
freq
u
e
ncy
.
commit
|
commitdiff
|
tree
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