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Version 2016.4
2017-08-10
C
a
rsten Kutzner
Corrected the P
D
F manua
l
t
o
reflect
that all
tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
C
arsten
Kutzner
A
d
d
ed missing
.
mdp file docume
n
tation fo
r
t
h
e enforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carsten Kutz
n
er
Fixed #2206 IMD interface mal
f
unct
i
ons
commit
|
commitdiff
|
tree
2017-06-16
Ca
r
st
e
n
K
ut
z
ner
Fixed a consistency check in
m
ake_edi for flooding
commit
|
commitdiff
|
tree
2016-11-16
Car
s
t
e
n Kutzner
Increased
the
de
f
ault reset step
t
o
1
500 in gmx tune_p
m
e
commit
|
commitdiff
|
tree
2016-11-15
C
a
rsten Kutzne
r
Fi
x
ed typo in membed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Cars
t
en Kutzner
Corrected value of electric
c
onver
s
ion factor f
in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Ca
r
sten Kutzne
r
Clean-u
p
c
ode f
o
r swapco
o
r
d
s
.
commit
|
commitdiff
|
tree
2016-03-18
Carst
e
n
Ku
t
zner
Clar
i
fied license text in the
.
tex
manual
commit
|
commitdiff
|
tree
2016-03-17
C
a
rsten Kutzner
Fix membed i
n
itialization
commit
|
commitdiff
|
tree
2016-02-18
Carsten K
u
tzner
Small
u
pdate to reference
m
an
u
al
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Changed norm(
.
.
.
)
> 0 condition to norm2(
.
.
.
) > 0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
C
a
rsten K
u
t
zn
e
r
Improved
/
en
l
arged
Fig
.
4
.
9
i
n
manual
for better rea
d
abilit
y
commit
|
commitdiff
|
tree
2016-01-20
C
a
rsten Kutzner
Made g_tune_pme work with -cpi -deffnm
c
ombinatio
n
commit
|
commitdiff
|
tree
2015-11-17
C
a
r
s
ten Kutzner
Fixed
-npstring command
l
i
ne argument in g
m
x
t
u
ne_p
m
e
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzner
Ion/w
a
ter po
s
iti
o
n sw
a
pping for multi
p
le ion types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
C
a
r
sten Kutzner
Described the computational elect
r
ophysi
o
logy
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carste
n
Kutzner
E
xtra opti
o
ns for compu
t
ational electrophysiology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Code
c
leanup in swapcoord
s
.
c
pp
commit
|
commitdiff
|
tree
2015-10-02
C
ar
s
ten
K
utzner
Fixed a bug
i
n computational electro
p
hysiolog
y
with DD
commit
|
commitdiff
|
tree
2015-07-15
Carsten Kutz
n
er
Re
m
o
ved information about obs
o
lete
.
edo file format
commit
|
commitdiff
|
tree
2014-12-09
Carsten K
u
tzner
Make tune_pm
e
u
nder
s
tand
t
he "-nsteps" option
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten
Kutzner
F
ixed a typo in the man
u
al
.
commit
|
commitdiff
|
tree
2014-11-12
Carsten
K
utzner
Updated some
.
mdp
file
variables
t
o use "-" inste
a
d
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Cars
t
e
n
Kutzne
r
F
ix
o
rder of E
D
/swap
b
l
o
cks during checkpoint reading
.
commit
|
commitdiff
|
tree
2014-10-01
Carsten Ku
t
zner
Allow gmx tune_
p
me to s
k
ip
t
h
e
c
heck for command-
l
i
n
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
C
a
rsten
K
u
tzner
F
ixed ou
t
p
ut of
eig
e
nvalues i
n
g_covar
.
Fixe
s
#
1575
commit
|
commitdiff
|
tree
2014-06-27
Ca
r
sten K
u
tzner
Remove o
b
sole
t
e
pull-
g
eometry option 'posi
t
ion' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten
K
utzn
e
r
R
e
-use gmx_wit
h
in_
t
ol from math
/
utilities in
s
tead of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carste
n
Kutzne
r
Fix documentation of swap/enu
m
s
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten Ku
t
zner
Fix docu
m
enta
t
ion
i
ssues for i
n
teractive MD mo
d
u
l
e
.
commit
|
commitdiff
|
tree
2014-03-26
Car
s
ten K
u
tzner
Documentat
i
on hous
e
-
k
eep
i
ng in file swapcoor
d
s
.
c
commit
|
commitdiff
|
tree
2014-03-14
Ca
r
sten
K
u
tzn
e
r
Avoid cross produc
t
w
i
th zero v
e
ctor in rotational
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kut
z
ner
The
van der
Waals radius must equal
t
he
Coul
o
mb rad
i
u
s
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
S
m
all en
h
anc
e
ment of c
o
mputat
i
o
nal ele
c
tro
p
hysiolog
y
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten
Kutzner
Al
l
o
w
for
"computation
a
l
e
lec
t
r
o
physiology
"
simulation
s
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Cars
t
en
K
utzner
M
o
ve pull
code to separat
e
subdirect
o
ry
commit
|
commitdiff
|
tree
2014-01-11
Carsten
K
utzner
Move
e
s
sent
i
a
l
dynamics
/ floo
d
ing code to separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Car
s
ten Kutzner
Re
a
d essential dynamics
data f
r
om
c
heckpoint at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
R
e
moved a few ty
p
o
s in th
r
ee German q
u
otes
.
commit
|
commitdiff
|
tree
2013-12-26
C
a
r
s
ten Kutzner
Pass
on default
v
alue
of
r
a
d
step
i
n mak
e
_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten Kutzner
E
s
s
en
t
ial dy
n
amics: m
o
ve bNeedDoEdsam e
v
aluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Cars
t
en Kutzner
Fixed ess
e
ntia
l
dyn
a
mic
s
(ED)
c
ontinua
t
ion from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
C
a
r
s
ten
Kutzner
Properly finalize M
P
I on mdru
n
-v
e
rsi
o
n
.
F
ixes #1313
commit
|
commitdiff
|
tree
2013-06-26
C
a
rsten Kutzn
e
r
F
ix
e
d -np
s
t
r
ing command line argument in g_tune_pme
commit
|
commitdiff
|
tree
2013-05-28
Carsten
Kutzner
Fixed calcu
l
ation
o
f slab bu
f
fer size
f
or fl
e
xible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten K
u
tzner
Fix for
a
rare cond
i
t
i
o
n in flexible rotation potentials
.
commit
|
commitdiff
|
tree
2013-05-27
Car
s
ten Kutzner
Code cleanup in enforced rota
t
ion module
,
r
e
move war
n
ings
.
commit
|
commitdiff
|
tree
2013-05-16
Carsten Kutzner
Choose th
e
PBC image of ea
c
h
rotation grou
p
atom de
p
endi
n
g
commit
|
commitdiff
|
tree
2013-04-29
Carsten Kutzner
Evaluate enfor
c
ed ro
t
ation
potenial with Ver
l
et, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten Kutzner
Essential dynamics: fixe
d
legend in ED
.
x
v
g output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Ku
t
zner
Made g_tune_pme work
with 4
.
6 if user sets "-p"
com
m
and
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten Kutzner
Fix
e
d t
h
e
MPI recognition string in g
_
tune_pme
commit
|
commitdiff
|
tree
2013-01-22
Carsten Kutzner
Mo
v
ed
a
few co
m
ments b
a
c
k into p
o
sitio
n
commit
|
commitdiff
|
tree
2013-01-17
Cars
t
en
Kutzne
r
Added n
o
te about
m
ake_edi and fl
o
od
i
ng in ED
p
ar
a
graph
commit
|
commitdiff
|
tree
2013-01-16
C
a
r
st
e
n
K
utzner
Made g_tun
e
_pme work correc
t
ly aga
i
n with
thread-M
P
I
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten Kutzner
E
ssential
d
yn
a
mic
s
output
f
ile n
o
w
i
n
.
xvg
f
ormat
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzner
Small fix for g_tune_p
m
e
commit
|
commitdiff
|
tree
2012-12-20
Carsten Ku
t
zn
e
r
Esse
n
ti
a
l dynami
c
s
: fix
e
d
r
estarts when ED
group has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Cars
t
en Kutzner
M
a
de
g
_
t
u
ne_p
m
e wo
r
k correctly when ir->in
i
t_step > 0
commit
|
commitdiff
|
tree
2012-10-16
Carsten K
u
tzn
e
r
Made g_
t
un
e
_pme r
e
ad (ns
/
day)
f
r
om 4
.
6 md
.
log output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
C
arsten Kutzner
Removed obsolet
e
hint in error mess
a
ge
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten Kutzner
Fixed essential dynamics
/
floodin
g
g
roup PBC ser
i
al
commit
|
commitdiff
|
tree
2012-08-06
Carst
e
n Kut
z
ner
Fixed c
a
l
c
ulatio
n
of proje
c
tio
n
for STA
R
and/or SO
R
I
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kutzner
Add
e
d comment in get_str
u
cture a
b
out w
h
ic
h
s
t
ructures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
F
ixed seg
v
in e
s
sen
t
ial
d
ynamics
mod
u
le
commit
|
commitdiff
|
tree
2012-07-06
Carsten K
u
tzner
Enf
o
rced rotation: PBC
/
restart fix
commit
|
commitdiff
|
tree
2012-06-11
Car
s
ten Kutz
n
e
r
Small fix for g_t
u
ne_pme
commit
|
commitdiff
|
tree
2012-05-23
Carsten
K
utzner
R
evised g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kutzner
Merge "Improv
e
d
w
arning note w
i
t
h
DD and periodic m
o
lecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten K
u
tzne
r
New
tool th
a
t extracts dye dynami
c
s from
t
raje
c
tories
commit
|
commitdiff
|
tree
2011-12-20
Car
s
t
e
n Kutzn
e
r
Ad
d
ed -dhdl t
o
tpr
f
ile list, fi
x
es #855
commit
|
commitdiff
|
tree
2011-12-19
Ca
r
sten Kutzner
Enfo
r
ced
r
o
tation
commit
|
commitdiff
|
tree
2011-11-22
C
a
rsten Ku
t
zner
Actual
l
y -cpi and -bc
p
o mus
t
not
b
e identical
commit
|
commitdiff
|
tree
2011-10-31
Carsten Kutzner
Fixed bug #830
(seg
v
in do_
d
ssp)
commit
|
commitdiff
|
tree
2011-08-31
Carsten
Kutzner
Remov
e
s
e
gv in
xpm2ps,
fixes #611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kutz
n
er
Re
m
ove
s
egv in
x
pm2ps, fixes #611
commit
|
commitdiff
|
tree
2011-08-25
Carsten Ku
t
zner
Instead
o
f
a segv, mdrun no
w
gives an error ms
g
if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carste
n
Kutzner
Typ
o
.
commit
|
commitdiff
|
tree
2011-07-29
Ca
r
sten Kutzner
Fixed ca
l
culation
o
f
max and min number of PME
-
only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carsten
K
u
tzner
Removed old-fashioned MPE logging code
commit
|
commitdiff
|
tree
2011-07-11
Ca
r
sten Kut
z
n
er
A
dded tw
o
m
i
ssin
g
h
e
ade
r
s
commit
|
commitdiff
|
tree
2011-07-06
Carsten Kutzner
A
d
ded globsig
.
h to
in
c
l
u
de/type
s
/Ma
k
e
f
ile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Kutzn
e
r
Floo
d
ing as
h
ar
m
.
r
es
t
raint: Ab
o
rt w
h
e
n
origin position
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Ca
r
sten Kutzner
Che
c
ks f
o
r zero
-
mass a
t
oms in E
D
, bett
e
r or
d
ering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Cars
t
en Kutzner
Fixed w
r
ong error message when using
f
looding
code
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
C
a
r
s
ten Kutzner
Fixed b
u
g #714:
d
eprecated str
u
cture in
getti
m
eofday
commit
|
commitdiff
|
tree
2011-02-25
Carsten
K
utzner
Corre
c
t
ed out
p
u
t
of a warnin
g
mes
s
age
.
commit
|
commitdiff
|
tree
2011-02-25
Carsten Kutzner
Ad
d
e
d
the -fix
option to
g
_tune_p
m
e for t
u
n
i
n
g
of rcoulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
Carsten
K
utzn
e
r
Enfo
r
c
e
d rotation: fix comp
i
ler warning
commit
|
commitdiff
|
tree
2011-02-16
Cars
t
en Kutzne
r
M
er
g
e bra
n
ch 'release-4-5-pa
t
ches'
commit
|
commitdiff
|
tree
2011-02-16
Carst
e
n
K
utzne
r
Merge branch '
r
elease-4-5-
p
atches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
Cars
t
e
n
Kutzner
Fixe
d
int overflow happenin
g
in g
e
nio
n
when
n
umber
.
.
.
commit
|
commitdiff
|
tree
2011-01-13
Ca
r
sten Kutzn
e
r
E
n
forced
rotation: ad
d
ed
f
it type 'potential'
commit
|
commitdiff
|
tree
2011-01-04
Carsten K
u
tzner
Me
r
ge b
r
a
n
c
h
'release-4-5-patche
s
'
commit
|
commitdiff
|
tree
2010-12-02
Ca
r
sten Ku
t
z
ner
M
erge b
r
anch 'r
e
le
a
se-4-5-patches'
commit
|
commitdiff
|
tree
2010-11-30
Carsten Kutzner
Mer
g
e branch 'master' of git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-11-26
Carsten K
u
tzner
Enforce
d
rotatio
n
: fixed
torque calcul
a
tion for FLEX
.
.
.
commit
|
commitdiff
|
tree
2010-11-23
Cars
t
e
n
Kutzn
e
r
Merge branch
'
master' of git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-11-23
Carsten Kut
z
n
er
Enforc
e
d rotation: code cleanup
commit
|
commitdiff
|
tree
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