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Fixes for Intel and container build fixes
2020-08-28
Carsten Kut
z
ner
U
pdated a
n
o
u
tdated l
i
nk
commit
|
commitdiff
|
tree
2019-10-02
Carsten Kutzn
e
r
Update
t
he www link to the Do
x
ygen
documentati
o
n in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
C
a
rsten Kutzn
e
r
Update the
w
ww
li
n
k to the Doxy
g
en documentat
i
on in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
Carsten Ku
t
zner
Move ForcePro
v
iders cl
a
ss int
o
th
e
gm
x
namespace
commit
|
commitdiff
|
tree
2019-09-30
Ca
r
sten Kutzner
Correcte
d
a few t
y
pos in docume
n
tat
i
on and comments
commit
|
commitdiff
|
tree
2019-04-04
Carsten Ku
t
zner
E
ar
l
y exit from mdrun if group
scheme is detected in
.
.
.
commit
|
commitdiff
|
tree
2018-05-10
Cars
t
e
n Kut
z
ner
Introduce helper classes for force provider input and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carsten Kutzner
Fix a
few
t
ypos in SIM
D
documentation
commit
|
commitdiff
|
tree
2017-12-20
Ca
r
s
ten K
u
tzne
r
Destruct MDModul
e
s/force providers prior to calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
C
a
rsten
Kutzner
Fix electr
i
c fi
e
ld
.
md
p
documentation
commit
|
commitdiff
|
tree
2017-08-10
C
ar
s
ten Kutzn
e
r
C
o
rrected the PD
F
man
u
al to reflect that al
l
tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
C
a
rsten Kutzner
Added
missing
.
mdp file
documentation for the en
f
or
c
ed
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten Kutzner
A
d
ded missi
n
g
.
mdp file
documentation
f
or the
enforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carst
e
n Kut
z
ner
Fixed #2206 IMD interfac
e
malfu
n
ct
i
on
s
commit
|
commitdiff
|
tree
2017-06-16
Car
s
ten Kutzner
Fixed a
c
o
n
s
i
stency
c
h
e
c
k in
make
_
edi for f
l
ooding
commit
|
commitdiff
|
tree
2017-06-09
Carsten Ku
t
z
n
er
Mo
v
e
d ess
e
n
tial dynamics initializa
t
ion call into do_md()
commit
|
commitdiff
|
tree
2017-06-09
Ca
r
sten K
u
tzner
Adopt a
n
d
d
ocument implementat
i
on pol
i
cy for MD modules
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kutzner
Minor header
f
ile
cleanup
i
n
ED, IMD and Co
m
pEL mo
d
ules
commit
|
commitdiff
|
tree
2017-04-19
Carste
n
K
u
tzner
Remove unused fo
r
w
a
rd declarat
i
ons of t_commr
e
c in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Carsten Kutzner
Rem
o
v
e
unne
c
ess
a
ry i
n
clud
e
commit
|
commitdiff
|
tree
2016-11-16
Carsten
Kutzne
r
Increased the defaul
t
reset step to 1500 in gmx tune_pme
commit
|
commitdiff
|
tree
2016-11-15
Carsten Kutzner
F
ixed typ
o
i
n
membed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
C
arsten Kutzner
C
o
rrected value of electric
c
onv
e
rsion factor
f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Cars
t
en Kut
z
ner
Clean
-
up co
d
e
f
or
s
wapcoords
.
commit
|
commitdiff
|
tree
2016-03-18
Ca
r
s
t
en K
u
tz
n
er
Clarifie
d
license text in the
.
tex manu
a
l
commit
|
commitdiff
|
tree
2016-03-17
C
a
rsten Kutzner
Fi
x
membed
i
nitialization
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutzn
e
r
Small update to referen
c
e
manual
commit
|
commitdiff
|
tree
2016-02-16
C
a
rs
t
en Kutzner
Changed
n
orm(
.
.
.
) >
0
condit
i
on to norm2
(
.
.
.
) > 0
i
n
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Car
s
te
n
Kutzner
Improved/enlarge
d
Fig
.
4
.
9 in manu
a
l for be
t
ter read
a
b
ility
commit
|
commitdiff
|
tree
2016-01-20
C
a
rsten Kutzner
Made
g
_t
u
ne_pme work with -cpi
-
deffnm
c
om
b
in
a
tion
commit
|
commitdiff
|
tree
2015-11-17
Car
s
ten Kutzner
Fix
e
d
-npstring
command lin
e
argument in gmx t
u
ne_pm
e
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzner
I
o
n/water position
swapping for multiple
ion typ
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutzner
Described the computational
el
e
ctrophysiology
.
m
dp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carste
n
Kutzne
r
E
x
tra optio
n
s
f
o
r co
m
putational e
l
e
ctrophysiology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Code
clea
n
up
in swapco
o
r
ds
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Carsten Kutzner
F
ixed a bug in computatio
n
al electrophysiology
w
ith D
D
commit
|
commitdiff
|
tree
2015-07-15
Carst
e
n
Kutzner
Removed
i
nformati
o
n a
b
out
obsolete
.
edo fi
l
e format
commit
|
commitdiff
|
tree
2014-12-09
Carsten Kutzner
Make tune_pme understand
the "-nsteps"
o
p
tion
.
F
i
xes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
C
a
rsten Kutzne
r
F
i
xed a typ
o
in the manual
.
commit
|
commitdiff
|
tree
2014-11-12
Carste
n
Kutzner
Update
d
some
.
mdp fil
e
variables to u
s
e "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carsten Kutzner
Fix order of ED/swap block
s
d
uring check
p
oint reading
.
commit
|
commitdiff
|
tree
2014-10-01
Carsten Ku
t
zner
Allow gmx tune_pm
e
to s
k
i
p
the check f
o
r command-
l
in
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Carsten Kutzn
e
r
Fix
e
d
o
utput of eigenvalu
e
s
in g_covar
.
Fixes #
1
575
commit
|
commitdiff
|
tree
2014-06-27
Carsten K
u
tz
n
er
Remove obso
l
ete pull-geometry opti
o
n 'position'
f
rom
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Cars
t
en
Kutzne
r
Re-use
gmx_w
i
thin_
t
ol
from
math/utilities
i
nstead
o
f
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carsten Ku
t
zner
F
i
x documen
t
atio
n
of swap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carst
e
n
K
utzner
Fix doc
u
mentation
issue
s
for inter
a
ctive
M
D mod
u
le
.
commit
|
commitdiff
|
tree
2014-03-26
Ca
r
s
ten Kutz
n
e
r
D
o
cum
e
n
t
ation house-keeping
in fil
e
swapcoor
d
s
.
c
commit
|
commitdiff
|
tree
2014-03-14
Ca
r
sten
Kutzner
Avoid cross
p
r
o
d
u
ct with zero ve
c
tor in
rot
a
tion
a
l
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kutzner
T
he
v
an der
W
aals radius must equal t
h
e Coulomb
radius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
C
arst
e
n Kutzner
Small
enh
a
nce
m
ent of
co
m
put
a
tiona
l
e
l
ectrophysi
o
logy
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Car
s
ten Ku
t
zn
e
r
Allow for "comp
u
tational
electrophysiology" simulations
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten Kutzner
Move pull code to
s
eparate subdirectory
commit
|
commitdiff
|
tree
2014-01-11
Carsten
K
u
tzne
r
Move
e
ssentia
l
dynamics
/ fl
o
oding code to s
e
p
arate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten Kutz
n
er
Rea
d
essen
t
ial dynami
c
s data from checkpo
i
nt
a
t corr
e
ct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
R
emove
d
a
few t
y
pos in three
Ge
r
man quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Cars
t
en
Kutzner
P
ass
o
n defa
u
lt valu
e
o
f rad
s
te
p
in make_ed
i
commit
|
commitdiff
|
tree
2013-12-25
Carsten Kutzne
r
Essential dynamics
:
move bN
e
ed
D
oE
d
sam evaluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
C
arste
n
Kutzner
Fix
e
d essential dynamics
(ED) co
n
tinuation from
.
c
p
t
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Carsten Kutzner
Prope
r
ly
fina
l
ize
M
P
I o
n
md
r
un -ve
r
s
ion
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-06-26
Carsten Kutzner
Fi
x
ed -npstring
c
omm
a
nd line argument in g_t
u
ne_pm
e
commit
|
commitdiff
|
tree
2013-05-28
C
ar
s
ten Kutzne
r
Fixed calculati
o
n of
slab
buffe
r
s
i
ze for
flexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzne
r
Fix for a rare condition in flexible
rotati
o
n potential
s
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten Kutzner
Co
d
e
c
l
e
anup in enforced
rota
t
ion module, r
e
mov
e
w
arnings
.
commit
|
commitdiff
|
tree
2013-05-16
Cars
t
e
n
Kutzn
e
r
Choose
t
he PBC image of
each rotation group at
o
m dependi
n
g
commit
|
commitdiff
|
tree
2013-04-29
Carsten Kutz
n
e
r
Evaluate en
f
orced rotation po
t
enial w
i
th V
e
rl
e
t
,
fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten
Kutzner
Es
s
ent
i
al dynamics:
f
ixed legend
in ED
.
xvg output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzner
Made g_tu
n
e_pme
w
o
r
k with 4
.
6 if u
s
er sets "-p" comman
d
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten
Kutz
n
er
Fixed the MPI recognition str
i
n
g
in g_tune_
p
m
e
commit
|
commitdiff
|
tree
2013-01-22
Car
s
t
en
Kutzner
M
ove
d
a
few comments
back
i
nto p
o
sit
i
on
commit
|
commitdiff
|
tree
2013-01-17
Carste
n
Kutzn
e
r
Added no
t
e about make_
e
di
and flooding in ED paragraph
commit
|
commitdiff
|
tree
2013-01-16
Carsten
K
utzner
Mad
e
g
_tune_pme wor
k
correc
t
ly again wit
h
thread
-
MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten
Kutzner
Esse
n
tial dyna
m
ics output file now in
.
xvg
f
o
rmat
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzner
Small fix for g_tune_pme
commit
|
commitdiff
|
tree
2012-12-20
C
arste
n
Ku
t
zner
Essential dynamics
:
fixed
restarts when
ED group has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kutzner
Made g_
t
u
ne_pme wor
k
correctly when ir->init_
s
t
ep
>
0
commit
|
commitdiff
|
tree
2012-10-16
C
a
rs
t
en Kutzn
e
r
Made g_tune_p
m
e
re
a
d (ns/day) from 4
.
6 m
d
.
l
og output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
Removed obsolete hint in e
r
ror
m
essage
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten
K
utzner
Fixed es
s
ential dynamics / flooding group PBC
serial
commit
|
commitdiff
|
tree
2012-08-06
Carsten K
u
tzner
Fix
e
d calculation of projectio
n
f
o
r STAR
a
n
d
/
or
SO
R
I
commit
|
commitdiff
|
tree
2012-08-06
Cars
t
en Kut
z
ne
r
Ad
d
e
d
c
omm
e
nt in get
_
structure abou
t
w
h
ich s
t
ructures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
C
a
rsten Kutzner
F
i
xed segv in essential dynamics modu
l
e
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kutzner
Enfo
r
ced
rotatio
n
: PBC/
r
estart fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Ku
t
z
n
e
r
Sma
l
l fi
x
for g_tune_
p
m
e
commit
|
commitdiff
|
tree
2012-05-23
Carsten Kutzn
e
r
Revised
g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kutzner
Merge "
I
mproved warning
n
ote with DD and periodic
molec
u
les
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
C
a
rsten Kutzner
New tool
that e
x
tracts dye d
y
namics
f
rom trajectories
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutz
n
er
Ad
d
ed -
d
hd
l
t
o
tpr file list, f
i
xes #85
5
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kut
z
ner
Enf
o
rced
r
otation
commit
|
commitdiff
|
tree
2011-11-22
Car
s
te
n
K
utzner
Actually
-c
p
i
a
n
d
-bcpo must not be
i
d
entical
commit
|
commitdiff
|
tree
2011-10-31
Carste
n
K
u
tzner
Fixed bug
#830 (seg
v
in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Carsten
Kutzner
R
e
m
o
v
e segv i
n
xpm2ps, f
i
xes
#611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kutzner
R
e
move
s
egv in xpm2ps
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-25
C
arste
n
Kutzner
Instead of a
segv,
m
d
ru
n
now
giv
e
s
a
n
e
r
ror msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
C
a
rsten
Kutzner
T
ypo
.
commit
|
commitdiff
|
tree
2011-07-29
Carste
n
K
u
tzner
Fixe
d
calculation of ma
x
and min
n
umbe
r
of
P
ME-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
C
a
rsten Kutzne
r
Removed old-fashio
n
ed MPE
l
oggin
g
c
o
de
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutzner
Added two missi
n
g headers
commit
|
commitdiff
|
tree
2011-07-06
Carsten Kutzn
e
r
Added globsig
.
h to i
n
c
lu
d
e/type
s
/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Cars
t
en Kut
z
ner
Flooding as ha
r
m
.
restraint
:
A
b
ort when origin pos
i
tion
.
.
.
commit
|
commitdiff
|
tree
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