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Added new testing code for normal mode analysis.
2015-11-14
Berk Hess
Optimi
z
ed the bonded thread for
c
e reduction
commit
|
commitdiff
|
tree
2015-11-13
David van der Sp
o
el
Moved genb
o
rn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
van der Spoel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid van der Spoel
Moved copyrite
.
* to
f
ilei
o
fro
m
g
m
xlib and le
g
ac
y
heade
r
s
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Moved pbc/
c
ut-off
r
elated utilities from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Davi
d
v
an der Spoel
Freed mem
o
ry in leg
a
cy statis
t
ics r
o
utines
.
commit
|
commitdiff
|
tree
2015-10-15
Be
r
k Hess
F
i
x
e
d nbnxn_
4
xN
perfo
r
mance regre
s
sion
commit
|
commitdiff
|
tree
2015-10-07
Berk H
e
ss
F
i
x bu
g
s
wi
t
h intermol interactio
n
s and DD
commit
|
commitdiff
|
tree
2015-10-03
David van
der Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
D
avid van der Spoel
Remov
e
d
s
imple
.
h from nb
_
kernel
_
avx
_
256_XX
commit
|
commitdiff
|
tree
2015-10-01
T
eemu Murtola
Enable t
i
me unit and se
l
ections
in IC
o
mman
d
LineOptionsMo
d
u
le
commit
|
commitdiff
|
tree
2015-09-30
D
avid
v
an der S
p
oel
Removed types/nblist
.
h a
n
d
type
s
/nsgrid
.
h f
r
om typ
e
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
v
id van der Spoel
Remov
e
d
types
/
mdat
o
m
.
h
fr
o
m typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der
Spoel
R
e
moved types
/
i
n
p
u
tre
c
.
h fr
o
m typedefs
.
h
a
nd
r
eleted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
M
ark Abraham
C
l
ean up of
t
ables code
commit
|
commitdiff
|
tree
2015-09-29
Mark Abraham
Move tab
l
es
.
c to new module and C++
commit
|
commitdiff
|
tree
2015-09-29
David va
n
der
Spoel
Fixes bug
i
n the co
m
putation of Coefficient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
Re
m
o
v
ed four
i
ncludes from lega
c
yh
e
ader
s
/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Davi
d
van der Spo
e
l
Removed lega
c
yhead
e
rs/t
y
pes/commrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
van der
S
poel
Remo
v
ed
<sys/t
y
pes
.
h> and "types/
c
onstr
.
h" from
typedefs
commit
|
commitdiff
|
tree
2015-09-08
David van der Spoe
l
Moved fu
n
ctions operating
o
n forcer
e
c t
o
separate h
e
a
d
er
.
commit
|
commitdiff
|
tree
2015-09-04
Ro
s
s
e
n
Apostolov
Converted essent
i
aldynamics module to C++
.
commit
|
commitdiff
|
tree
2015-09-02
Bé
l
a Voß
Avoid i
n
teger overf
l
ow
in gmx_wham
by usi
n
g gmx_int6
4
_t
.
commit
|
commitdiff
|
tree
2015-08-03
Dav
i
d
van der Spoel
Made output
from dump
i
ng neig
h
tborlists
e
asier to
r
ea
d
.
commit
|
commitdiff
|
tree
2015-07-29
Erik Lindahl
Moved another bunch of mdlib
u
t
ils to C++
commit
|
commitdiff
|
tree
2015-07-29
Erik
Lindahl
Upd
a
te naming standards to avo
i
d hungaria
n
notation
.
.
.
commit
|
commitdiff
|
tree
2015-07-24
Tee
m
u Murtola
R
e
name trnio
.
* to trrio
.
*
commit
|
commitdiff
|
tree
2015-05-12
Jochen Hub
OpenMP paralleliza
t
ion of g_
w
ham
commit
|
commitdiff
|
tree
2015-04-09
Da
v
id v
a
n der Spoe
l
Clarified comments f
o
r ti
m
e-dependent el
e
ctric field
s
.
commit
|
commitdiff
|
tree
2015-04-08
David van
d
er
S
poel
Fixed incorrect out
p
ut of gb
_
algorith as sa_algo
r
it
h
m
.
commit
|
commitdiff
|
tree
2014-10-28
David van de
r
S
p
oel
Even more refreshing quotes
.
commit
|
commitdiff
|
tree
2014-09-22
Mark Abraham
Mo
r
e quo
t
es
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
More quotes
commit
|
commitdiff
|
tree
2014-09-19
Teem
u
Murtola
Add s
u
ppo
r
t
for cumulative h
i
stograms
commit
|
commitdiff
|
tree
2014-09-17
D
a
vi
d
van der Sp
o
el
M
e
rge rel
e
ase-5-0 into
m
aster
commit
|
commitdiff
|
tree
2014-08-30
David
v
an der S
p
oe
l
Fixes issue with vsi
t
en
and verlet buffers
.
commit
|
commitdiff
|
tree
2014-06-25
Dav
i
d van der Spoel
A
dd
e
d che
c
k for domain de
c
omposit
i
on and shells
.
commit
|
commitdiff
|
tree
2014-06-22
David
van de
r
Spoel
Imp
l
emented fatal erro
r
for
n
stcalcene
r
gy!=1 with shells
.
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
M
a
de
s
hells wor
k
with the Verlet
sch
e
me
commit
|
commitdiff
|
tree
2014-06-12
Berk
Hess
Made g
m
xcheck -rmsd work again
with force
s
commit
|
commitdiff
|
tree
2014-06-12
E
rik Li
n
dahl
Make sure genres
t
r
uses the
d
isre_up2 pa
r
ameter
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Remo
v
e
d
und
o
cumented -map
a
nd -mdata
o
ptio
n
s f
r
o
m
g_sh
a
m
.
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Always write output from
g
enion
commit
|
commitdiff
|
tree
2014-06-11
D
a
v
id van
d
er Sp
o
el
Fixe
s
bug wher
e
-
e and -dt flags did not work anymore
.
commit
|
commitdiff
|
tree
2014-06-11
Berk H
e
ss
Made re
p
l_ex tim
e
step more read
a
ble
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtola
Improve (Selection|FileName)O
p
tionManager handli
n
g
commit
|
commitdiff
|
tree
2014-06-07
T
e
emu Murt
o
la
Rep
l
ace all command line
pa
r
sing with Op
t
ions
commit
|
commitdiff
|
tree
2014-06-07
Teemu M
u
rtola
Move
resi
d
u
etype
handli
n
g to its o
w
n
file
.
commit
|
commitdiff
|
tree
2014-06-07
T
e
emu Murtola
Remove su
p
port for
"old" index
file format
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lund
b
org
F
ix bug writin
g
TNG output from dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lu
n
dborg
Bug fi
x
in the TNG
l
ibrary to impr
o
ve
r
eading
.
commit
|
commitdiff
|
tree
2014-05-24
Mark Abrah
a
m
Move tools code t
o
where it is used
commit
|
commitdiff
|
tree
2014-05-18
Tee
m
u Murtola
Mov
e
3dview
.
* to programs/view/
commit
|
commitdiff
|
tree
2014-05-16
David van der Spoel
Fixes
a com
p
lica
t
e
d bug in g_anaeig
.
commit
|
commitdiff
|
tree
2014-03-17
Te
e
mu
M
urtola
Update m
a
nual analysis s
e
ction
commit
|
commitdiff
|
tree
2014-02-21
Nina F
i
sch
e
r
Added
new amber99sb-ildn-bsc0
f
orce field
.
commit
|
commitdiff
|
tree
2014-02-10
David
v
an der Spoel
Moved condit
i
o
nal cma
k
e code f
o
r vmdio
.
commit
|
commitdiff
|
tree
2014-01-19
Mark Abr
a
ham
C
l
ean up after gmxcpp
commit
|
commitdiff
|
tree
2013-12-23
Davi
d
van der Spoel
Fixed co
m
pilation issue du
e
t
o gcc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
David
v
a
n
der Spoel
Fixes #1312 uninitialized e
r
ror in g_enemat
.
commit
|
commitdiff
|
tree
2013-05-16
Da
v
i
d
van d
e
r Spoel
F
ixed two compilat
i
on iss
u
e
s
.
commit
|
commitdiff
|
tree
2013-05-02
David van
der Spoel
F
i
xes #1238
g
_hydorder do
e
s n
o
t call set_pb
c
.
commit
|
commitdiff
|
tree
2013-03-07
David
v
an der
Spoe
l
Fixes #1183 PBC b
u
g in g
_
m
i
ndist
commit
|
commitdiff
|
tree
2013-02-13
David v
a
n
der Spo
e
l
Plain text quote
s
.
commit
|
commitdiff
|
tree
2012-11-26
D
avid van
d
er Sp
o
e
l
F
i
xes #1035 Na
N
i
n
g_c
l
us
t
er output
.
commit
|
commitdiff
|
tree
2012-11-20
D
a
vid van
d
er
S
p
o
el
Fixes b
u
g
in g_hbond that makes i
t
p
roduce fat
a
l
er
r
o
r
.
commit
|
commitdiff
|
tree
2012-10-21
David van der Spoel
F
ixe
d
Bug #59
3
a
bou
t
memor
y
hole in trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
Da
v
id van der S
p
oel
Set r
e
turn value to FALSE (
0
) in estimate_dt
in libxd
r
f
.
c
commit
|
commitdiff
|
tree
2012-09-07
David van der Spoe
l
Adapted
NMR rela
t
e
d
data to n
e
w pdb format
.
commit
|
commitdiff
|
tree
2012-09-04
David van
d
er Spoel
Made tutori
a
l slightly le
s
s confusing
.
commit
|
commitdiff
|
tree
2012-08-16
Da
v
id van d
e
r Spoel
Opti
o
nal computat
i
on of fluct
.
p
rops in
g_energy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
David va
n
der S
p
oel
F
i
xed bug in free energ
y
calculation for Morse potenti
a
ls
commit
|
commitdiff
|
tree
2012-06-21
Da
v
id van
der S
p
o
e
l
Fixe
s
#961 - Shake rep
o
r
ts wron
g
error
commit
|
commitdiff
|
tree
2012-03-17
D
a
vid
v
an
der Spoel
Rem
o
v
e
d qhop f
i
les
f
rom this br
a
nch
.
commit
|
commitdiff
|
tree
2012-03-10
Dav
i
d van der Spoel
Vibration spectra from velocity ACF or
Normal m
o
des
.
commit
|
commitdiff
|
tree
2012-01-31
David
v
an der Spo
e
l
Ch
a
nged or
d
er of
parameters
in top file
commit
|
commitdiff
|
tree
2012-01-25
D
a
v
i
d va
n
der Spoel
Added two n
e
w
bonded fun
c
tions
.
commit
|
commitdiff
|
tree
2012-01-17
Davi
d
van der
Spoel
Repl
a
c
e
stderr by stdo
u
t
in editconf t
e
r
m
i
nal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David van der
Spo
e
l
Introdu
c
ed fa
t
a
l
er
r
o
r in gro
m
p
p for incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van
d
er Sp
o
el
Commente
d
out
par
t
of this new
prog
r
am
that was not
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
F
ix
e
d do
c
umentation issu
e
des
c
ribed i
n
redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Da
v
id van der
S
p
oel
Fixed
documentation i
s
sue described in re
d
mine
i
ssue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
D
avi
d
van d
e
r Spoel
F
ixe
d
compi
l
ation issues
commit
|
commitdiff
|
tree
2011-09-19
Dav
i
d van der Spo
e
l
R
esolved gerrit issue https://gerrit
.
gromacs
.
o
r
g/
#
ch
a
n
g
e,1
2
6
commit
|
commitdiff
|
tree
2011-09-13
David van der Spoel
Added warning
line
.
commit
|
commitdiff
|
tree
2011-07-20
David van der Spoel
Merge branch 'release-4
-
5-patches' of git@
g
i
t
.
gr
o
mac
s
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
Da
v
id v
a
n der Sp
o
el
Added in
i
t
i
alizatio
n
o
f
a
r
r
ays after srenew call
.
commit
|
commitdiff
|
tree
2011-07-20
D
a
vid
v
an der Spo
e
l
Added
in
i
tialization
of
a
rrays after sr
e
n
ew call
.
commit
|
commitdiff
|
tree
2011-07-02
David van der Spoe
l
M
erg
e
branch 'master' of git@git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2011-07-02
David van d
e
r
Spoe
l
Compi
l
ation fixes in gmx
_
density
.
c and histogr
a
m
.
cpp
commit
|
commitdiff
|
tree
2011-07-01
David van der Spoel
Merge branch 'release-4-5-patches' of git@g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der Spoe
l
M
e
r
g
e
b
ranch 'releas
e
-
4
-5-p
a
tches'
of g
i
t@g
i
t
.
g
r
o
m
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
Davi
d
van der
S
po
e
l
Added
g
_
d
o
s
t
arget
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
an der Sp
o
el
Further
p
atch
e
s
to fluctuation code and den
s
ity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van
d
er Spoel
Added c
o
mputation of A and U
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
v
an
d
er Spoel
Upd
a
ted, ma
d
e def
a
ult tolerance for bisector more string
e
nt
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der
S
poel
Fixe
d
weight functions and
added -du
m
p option (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
va
n
d
e
r Spoel
Updated
.
Fixed c
o
mp
u
tation of frequen
c
y
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Updated the eqn for computing Delta
.
Now get r
o
ughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Mul
t
ipli
e
d the DoS by the
timestep (between fram
e
s)
.
commit
|
commitdiff
|
tree
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