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GROMACS 2016 beta1 release
2016-04-14
Ca
r
s
t
e
n Ku
t
zner
Corrected
value of electric conversi
o
n factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
C
a
rsten Kutzner
Cl
e
an-up
c
ode
f
or swapcoords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten Ku
t
zner
Clarifie
d
license text in the
.
t
e
x manual
commit
|
commitdiff
|
tree
2016-03-17
Carsten Kutzne
r
Fix m
e
mbe
d
initialization
commit
|
commitdiff
|
tree
2016-02-18
C
arsten Kutzner
Small upd
a
te to reference manua
l
commit
|
commitdiff
|
tree
2016-02-16
Carsten K
u
tzner
Chan
g
ed norm(
.
.
.
) > 0
c
o
ndi
t
ion to n
o
rm2(
.
.
.
) > 0
i
n
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Cars
t
en
K
utzner
Improved/enlar
g
ed Fi
g
.
4
.
9 in manual for better
r
eadabili
t
y
commit
|
commitdiff
|
tree
2016-01-20
Carsten Kutz
n
er
M
ade g_tune_pme wo
r
k
wit
h
-cpi -def
f
n
m com
b
ination
commit
|
commitdiff
|
tree
2015-11-17
C
ars
t
en
K
u
t
z
n
e
r
Fixe
d
-nps
t
ri
n
g command line
a
rgument i
n
gmx tune_
p
me
commit
|
commitdiff
|
tree
2015-11-13
Carsten K
u
tzner
Ion/wa
t
er position sw
a
pping for mu
l
tip
l
e
ion t
y
pes
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
C
arsten Kutzner
Described
t
he computational e
l
ectrophysiolo
g
y
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Extra opt
i
ons for
computational electrophysiolo
g
y
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kut
z
n
e
r
Code c
l
ean
u
p
in swapc
o
ords
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
C
a
r
sten Kutzn
e
r
F
i
xed a b
u
g in computational
e
le
c
trophysiology
w
ith DD
commit
|
commitdiff
|
tree
2015-07-15
Car
s
t
en
Kutzner
Removed information about o
b
solete
.
edo file format
commit
|
commitdiff
|
tree
2014-12-09
Car
s
ten
K
utzner
Make tune
_
pme understa
n
d the
"-
n
ste
p
s" op
t
ion
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Ca
r
sten
K
u
t
zner
F
i
x
ed
a typo in the
m
anual
.
commit
|
commitdiff
|
tree
2014-11-12
Carsten
Kutz
n
er
U
p
dat
e
d some
.
m
d
p
file variables to
use "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Cars
t
en Kutzner
Fix order of ED
/
swap blocks during
checkpoint readi
n
g
.
commit
|
commitdiff
|
tree
2014-10-01
Car
s
ten Kut
z
ner
Allow gmx tu
n
e_pme to ski
p
the check for c
o
mm
a
nd-line
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Carsten Kutzner
Fixed ou
t
pu
t
of eigenv
a
lues
in g
_
c
ovar
.
Fi
x
es #1575
commit
|
commitdiff
|
tree
2014-06-27
C
arst
e
n Kutzner
Remove obs
o
le
t
e pull
-
geometry option '
p
osi
t
ion' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
C
arsten Kutzner
Re
-
use g
m
x_wi
t
hin_
t
ol from math/utilities instead of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carst
e
n Kutzn
e
r
Fix docum
e
ntation of swap/en
u
ms
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten Kutzner
Fix do
c
umentatio
n
issues for interactive M
D
mo
d
ule
.
commit
|
commitdiff
|
tree
2014-03-26
Carsten Kutzner
D
o
c
u
mentation house-keeping in file swapcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
C
a
rsten Kutzner
Avoid
c
ros
s
p
r
oduc
t
w
ith zero vector
i
n rotational
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carsten
Kutzner
The
van der Waals radius m
u
st equal th
e
Coulo
m
b
ra
d
ius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
Smal
l
enhancement
o
f co
m
p
u
tational electrophysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten Kutzner
A
llow for "computat
i
onal electroph
y
siology" simul
a
t
i
ons
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten Ku
t
zner
Mov
e
p
ull code to separate sub
d
irectory
commit
|
commitdiff
|
tree
2014-01-11
C
arsten Kutzn
e
r
Move esse
n
tial dynamics / flo
o
ding
cod
e
to separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
C
ar
s
ten Kutzner
Read essenti
a
l dy
n
amic
s
d
ata from checkpoint at
c
o
r
rect
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Cars
t
en Kutz
n
er
Removed a f
e
w typos in three G
e
rma
n
q
uot
e
s
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten Kutzner
P
ass o
n
defa
u
lt value of
r
a
d
step in
m
ake
_
edi
commit
|
commitdiff
|
tree
2013-12-25
C
a
r
s
t
en Kut
z
ner
E
s
sential dyna
m
ics: mo
v
e
b
N
eedDoEdsam evalu
a
tion to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Car
s
t
e
n Kut
z
ner
Fi
x
ed essentia
l
dy
n
amics
(
ED) continuation from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
C
a
rst
e
n Kutzner
Properly finalize MPI on m
d
run -versio
n
.
Fixes
#1313
commit
|
commitdiff
|
tree
2013-06-26
C
ar
s
ten Kutzne
r
Fi
x
ed -npstring command
l
i
n
e argu
m
ent in g_tune_pme
commit
|
commitdiff
|
tree
2013-05-28
C
ar
s
ten Kutzner
F
i
xe
d
ca
l
culation of sl
a
b buffer
size
f
o
r
flexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Cars
t
en
K
ut
z
n
er
F
i
x
f
or
a rare
condition in flex
i
b
l
e
r
o
tati
o
n potentials
.
commit
|
commitdiff
|
tree
2013-05-27
Ca
r
st
e
n K
u
tz
n
er
C
o
de cleanup i
n
enforced
rotation module, r
e
m
ove warnings
.
commit
|
commitdiff
|
tree
2013-05-16
Car
s
t
en Kutzner
Choose the PBC image of each rotation group
a
tom
d
epen
d
in
g
commit
|
commitdiff
|
tree
2013-04-29
Carst
e
n
K
ut
z
ner
Evaluate enforced r
o
tation poteni
a
l
wi
t
h
Verlet, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carste
n
K
u
tzner
Essent
i
al dynam
i
cs: fixed legend in ED
.
xvg
o
u
tp
u
t
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutz
n
er
Made g_tune_pme
work w
i
th 4
.
6 if user sets "-p" command
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
a
rsten Kut
z
ner
Fixed the M
P
I r
e
cognition string in g_tu
n
e_pme
commit
|
commitdiff
|
tree
2013-01-22
Carst
e
n Kutzn
e
r
M
oved a few commen
t
s
back into pos
i
tion
commit
|
commitdiff
|
tree
2013-01-17
Carsten Ku
t
zn
e
r
Added note ab
o
ut
m
ake_edi and
flooding in ED
p
ar
a
graph
commit
|
commitdiff
|
tree
2013-01-16
Cars
t
en Kutzner
M
a
de g_tune_pme
work co
r
rectly again with
thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
C
a
rsten Kutzne
r
Es
s
ent
i
al dy
n
amic
s
output file now in
.
xvg format
commit
|
commitdiff
|
tree
2012-12-20
Carst
e
n Kutzne
r
Small fix for g_tu
n
e_p
m
e
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzner
Ess
e
ntial
dynamics: fixed res
t
arts w
h
en ED group has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carste
n
K
utzner
Made g_tune_pme work correctly when
i
r->init_step >
0
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzne
r
M
ad
e
g_tun
e
_p
m
e read (ns/day) from 4
.
6
md
.
l
o
g output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten
Kutzn
e
r
Re
m
oved obsolete hi
n
t
in error
m
ess
a
ge
.
commit
|
commitdiff
|
tree
2012-08-07
C
a
r
sten Kutz
n
er
F
i
x
ed essenti
a
l dyn
a
mics / flooding grou
p
PBC seria
l
commit
|
commitdiff
|
tree
2012-08-06
Cars
t
e
n
Kutzn
e
r
Fix
e
d calculation of projection f
o
r STAR and/or SORI
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kut
z
ner
Added comment in get_s
t
ructure about which structur
e
s
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
F
ixed segv i
n
es
s
ential dyna
m
ics m
o
dul
e
commit
|
commitdiff
|
tree
2012-07-06
Carsten K
u
tzn
e
r
E
n
for
c
ed rota
t
ion: PBC/restart fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Kutz
n
e
r
Small fi
x
for g_tu
n
e_pm
e
commit
|
commitdiff
|
tree
2012-05-23
C
arsten Kut
z
ner
Re
v
ised g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
Ca
r
sten
Kutzner
Merge "Im
p
rove
d
warning n
o
te with
DD
and
p
eriodic mo
l
ecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Ca
r
s
t
en Kutzner
N
e
w too
l
that extract
s
dye dynamics from traject
o
ri
e
s
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutzn
e
r
Ad
d
ed -dh
d
l
to
tpr file list
,
fixes #855
commit
|
commitdiff
|
tree
2011-12-19
Carsten
K
utzner
Enforced
r
o
tation
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutzner
Actually -cpi and -bcpo mus
t
n
o
t be identical
commit
|
commitdiff
|
tree
2011-10-31
Ca
r
sten Kutzner
Fixed bug #83
0
(segv in do_ds
s
p)
commit
|
commitdiff
|
tree
2011-08-31
C
arst
e
n Kutzn
e
r
R
emove segv in xpm2ps, fixes #611
commit
|
commitdiff
|
tree
2011-08-26
Carst
e
n Kutz
n
er
Remo
v
e segv in xpm2ps, fixes #6
1
1
commit
|
commitdiff
|
tree
2011-08-25
Carsten Kutzner
I
n
ste
a
d of a
s
egv, mdrun now gives an error msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten Kutzner
T
ypo
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten Kutz
n
er
Fi
x
ed
c
alculation of
m
ax and min number of PME-
o
nly
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
C
arsten Kutzner
Remove
d
old-fashioned MPE logging code
commit
|
commitdiff
|
tree
2011-07-11
Ca
r
sten
K
u
t
zner
A
d
ded t
w
o missing h
e
aders
commit
|
commitdiff
|
tree
2011-07-06
Ca
r
s
t
en Kutzner
Adde
d
globsig
.
h to include/types/Ma
k
efile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten
K
utzn
e
r
Floodin
g
as
ha
r
m
.
r
e
straint: Abort when
o
r
i
g
i
n po
s
ition
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
C
heck
s
for zero-mass
a
toms in ED, bet
t
er orderin
g
o
f
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten
K
utzn
e
r
Fixed
w
rong error message when using
f
l
o
oding c
o
de
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Carsten K
u
tz
n
er
F
i
x
ed bug #
7
14: deprecated structure in ge
t
timeofday
commit
|
commitdiff
|
tree
2011-02-25
Carsten Kut
z
ner
C
orrected o
u
tput of
a
war
n
ing message
.
commit
|
commitdiff
|
tree
2011-02-25
C
arsten Ku
t
zne
r
Added
t
he -fix op
t
ion to g_tune_pm
e
for tuning of rco
u
lom
b
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
Carste
n
Kutzner
E
nforced r
o
tatio
n
: fix co
m
piler warning
commit
|
commitdiff
|
tree
2011-02-16
Carsten
K
utzner
M
e
r
g
e bra
n
c
h 'release-4-5-patches'
commit
|
commitdiff
|
tree
2011-02-16
Carsten Kutzner
Merge bra
n
ch 're
l
ease-4-5
-
patches' o
f
git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
Carste
n
Ku
t
zner
F
i
xed int overf
l
ow h
a
p
p
e
ning
in genion when number
.
.
.
commit
|
commitdiff
|
tree
2011-01-13
Carste
n
Kutzne
r
Enfor
c
ed
r
otation: ad
d
ed fit type 'potential'
commit
|
commitdiff
|
tree
2011-01-04
Carsten
Kutz
n
er
Merge branch
'
release-4-5-patches
'
commit
|
commitdiff
|
tree
2010-12-02
C
a
rste
n
Kut
z
n
er
Merge bra
n
ch 'r
e
lease-4-5
-
patches'
commit
|
commitdiff
|
tree
2010-11-30
C
a
rst
e
n
Kutzner
Merge branch
'ma
s
ter' of
g
i
t
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-11-26
Carsten
Ku
t
zn
e
r
E
n
f
o
rced
r
otation:
fixed to
r
q
ue ca
l
c
u
lation
for
F
L
EX
.
.
.
commit
|
commitdiff
|
tree
2010-11-23
Carsten K
u
tzner
Merge b
r
anch 'mas
t
er'
of git
.
g
romacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-11-23
Cars
t
e
n Kut
z
ne
r
E
nfor
c
ed
r
o
tation:
c
ode cl
e
anup
commit
|
commitdiff
|
tree
2010-11-18
Car
s
te
n
K
utzner
B
ett
e
r de
s
criptio
n
of rot
a
tio
n
optio
n
s
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kutzner
Re
m
oved unneces
s
ar
y
include
commit
|
commitdiff
|
tree
2010-11-17
C
a
rs
t
en Kutzner
Me
r
ge bra
n
ch
'
rotat
i
on
'
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kutzner
Merge
branch 'r
e
l
eas
e
-4
-
5-pat
c
hes
'
commit
|
commitdiff
|
tree
2010-11-15
Carsten Kut
z
n
e
r
Merge branch 'rota
t
i
on-4-5' into rota
t
ion
commit
|
commitdiff
|
tree
2010-11-15
Car
s
t
e
n
Kut
z
ne
r
E
n
forced rotation: def
i
n
e
Gaussian norm
commit
|
commitdiff
|
tree
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