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Make gmx_multisim_t a C++ object
2019-04-04
C
arsten Kutzn
e
r
Early
e
xit fro
m
mdrun if group
s
ch
e
m
e is detected in
.
.
.
commit
|
commitdiff
|
tree
2018-05-10
Car
s
ten Kutzner
In
t
roduce
h
elper classes
for for
c
e provider
i
nput and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carst
e
n Kutzner
Fix a few
typos in SIMD documentation
commit
|
commitdiff
|
tree
2017-12-20
Carste
n
K
u
tzner
D
e
struct
M
DModu
l
e
s
/force providers pri
o
r to calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
C
a
rsten Kutzne
r
Fix elect
r
ic field
.
m
dp d
o
c
u
mentation
commit
|
commitdiff
|
tree
2017-08-10
Carsten Kutzner
Corr
e
ct
e
d the PDF manual t
o
reflect
t
hat a
l
l
tool
s
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten Kutzner
Added mis
s
ing
.
md
p
file documentation for th
e
enforced
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carste
n
Kutzner
Added
missing
.
m
dp
file
d
ocum
e
nt
a
tion for the enforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
C
a
r
sten Kutzner
Fixe
d
#2206 I
M
D int
e
rfac
e
m
a
l
functions
commit
|
commitdiff
|
tree
2017-06-16
C
a
rsten Kutzner
Fix
e
d a consistency check
in make_edi for
flooding
commit
|
commitdiff
|
tree
2017-06-09
Cars
t
en Kutzner
Moved
essential
dynamics
i
nitialization cal
l
in
t
o d
o
_
m
d
()
commit
|
commitdiff
|
tree
2017-06-09
Carsten Ku
t
zner
A
d
op
t
a
n
d
do
c
umen
t
impleme
n
tation
p
olicy
for MD modules
commit
|
commitdiff
|
tree
2017-04-29
Ca
r
sten
Kutzner
Minor header file cleanup in
E
D, IMD and CompEL modules
commit
|
commitdiff
|
tree
2017-04-19
Carsten Kut
z
n
er
R
e
mo
v
e unus
e
d forward decl
a
ra
t
io
n
s of t_commrec
in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
C
arsten Kutzner
Remove unnecessar
y
include
commit
|
commitdiff
|
tree
2016-11-16
Carsten
K
u
t
z
n
er
Incr
e
ased t
h
e
d
efault rese
t
step to
1500 in
gmx tune
_
pme
commit
|
commitdiff
|
tree
2016-11-15
Cars
t
en Kutzner
Fixed
t
ypo in
m
e
mbed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Carsten Kutz
n
er
Corr
e
cted value of
e
l
ectric conversion f
a
ctor f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzne
r
Clea
n
-up c
o
de for s
w
apcoords
.
commit
|
commitdiff
|
tree
2016-03-18
Carst
e
n Kut
z
ne
r
C
larifi
e
d li
c
en
s
e
text
i
n t
h
e
.
tex
manual
commit
|
commitdiff
|
tree
2016-03-17
C
ar
s
ten
K
utzner
Fix memb
e
d initi
a
lization
commit
|
commitdiff
|
tree
2016-02-18
Carsten Ku
t
zner
Small update to reference manu
a
l
commit
|
commitdiff
|
tree
2016-02-16
C
a
rs
t
en Kut
z
ner
Changed
n
or
m
(
.
.
.
)
>
0 conditio
n
to norm2(
.
.
.
) > 0
i
n
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Improv
e
d/
e
nlarged Fig
.
4
.
9 in manual
for better
readability
commit
|
commitdiff
|
tree
2016-01-20
Carst
e
n Kutzner
Made
g_tune_pme work with -cpi -deffnm c
o
mbina
t
i
on
commit
|
commitdiff
|
tree
2015-11-17
Ca
r
sten Kutzne
r
Fi
x
ed -np
s
tring comm
a
n
d line argument in gmx t
u
ne_pme
commit
|
commitdiff
|
tree
2015-11-13
Car
s
te
n
K
utzner
I
on/water position swapp
i
ng for mult
i
p
le
i
on t
y
pes
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutzner
De
s
c
r
ibed the computational
elect
r
ophysiology
.
md
p
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten
K
utzner
E
x
t
r
a
o
ptions fo
r
computational electrophys
i
o
l
ogy
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Code cl
e
anup in swapc
o
ords
.
cp
p
commit
|
commitdiff
|
tree
2015-10-02
Carsten K
u
tzner
Fixed
a
b
ug
in computational electrophysiolog
y
w
i
th DD
commit
|
commitdiff
|
tree
2015-07-15
Ca
r
st
e
n Kutzner
Re
m
oved inf
o
rmation
about obs
o
le
t
e
.
edo file format
commit
|
commitdiff
|
tree
2014-12-09
Carsten Kutzner
Make tune_pme
understand the "-ns
t
eps"
option
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten Kutzner
Fixed a typo in the manual
.
commit
|
commitdiff
|
tree
2014-11-12
C
ar
s
ten
K
utzner
Updated
s
o
me
.
mdp file variables
to use "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carsten Kutzner
Fix o
r
der of ED/swap block
s
during checkp
o
in
t
reading
.
commit
|
commitdiff
|
tree
2014-10-01
C
a
r
st
e
n
Kut
z
n
er
A
llow gmx tune_pme
to s
k
i
p
the check for comm
a
nd-l
i
ne
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Cars
t
e
n
Kutz
n
e
r
Fi
x
ed output of eigenv
a
lues in g_covar
.
Fixes #1575
commit
|
commitdiff
|
tree
2014-06-27
Carste
n
Kutzn
e
r
Remove obsolete pull-g
e
ome
t
ry option '
p
osi
t
ion' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carst
e
n Ku
t
zner
Re-use gmx_wi
t
hin_tol from m
a
th/ut
i
lities instead o
f
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carsten Kutzner
Fix do
c
um
e
n
t
ation of
swap
/
enums
.
h
commit
|
commitdiff
|
tree
2014-03-28
C
a
rsten Kutzner
F
ix documen
t
a
t
ion issue
s
for interactive MD modu
l
e
.
commit
|
commitdiff
|
tree
2014-03-26
Carsten Kutzn
e
r
Documentation
h
ouse-keeping
i
n
f
ile swa
p
coo
r
ds
.
c
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kutzner
Avo
i
d cross product with zero vec
t
or in rotatio
n
a
l
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Ca
r
s
ten
Kut
z
ner
T
he v
a
n
der
W
aa
l
s radius must equa
l
the Coulomb radius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten K
u
tzner
Sm
a
ll enhancement o
f
compu
t
ation
a
l electrop
h
ysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten Kutzner
Allow for "
c
o
mputatio
n
al electro
p
hys
i
o
l
ogy" simulations
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
C
a
rste
n
Kutzner
Mo
v
e pul
l
code to sep
a
ra
t
e
subdirect
o
ry
commit
|
commitdiff
|
tree
2014-01-11
Carst
e
n Kutzner
Move
e
ss
e
ntial dynamics /
f
looding cod
e
to separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten Kutzner
Read essential d
y
nam
i
cs data fro
m
ch
e
ckpoint at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
C
arsten Kut
z
n
er
Re
m
oved a few typos
in three Germ
a
n quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten K
u
tzner
Pass
on default value o
f
r
a
dste
p
i
n make_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten
K
u
tzner
Esse
n
tial dynamic
s
:
mov
e
b
NeedDoEdsam evaluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
C
arsten Kutzner
Fixe
d
essent
i
al dynamics
(
ED) con
t
i
n
uation f
r
o
m
.
cp
t
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Carst
e
n Kutzner
Properly finalize MPI on mdrun -versi
o
n
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-06-26
C
a
rsten K
u
tz
n
er
Fixed -npstring
c
o
mmand line argument in g_
t
une_pme
commit
|
commitdiff
|
tree
2013-05-28
C
a
rsten
Kutzner
Fixed
calcu
l
ation
o
f slab buf
f
er size for f
l
e
xible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
C
arst
e
n K
u
tzner
Fix for
a rare condit
i
o
n in
flexible rota
t
i
o
n po
t
ential
s
.
commit
|
commitdiff
|
tree
2013-05-27
C
a
rst
e
n Ku
t
z
ner
Code cleanup in
e
n
forced rotati
o
n
m
o
d
ule, remove warning
s
.
commit
|
commitdiff
|
tree
2013-05-16
Carsten K
u
tzner
Choos
e
the PBC image of each rotation group atom de
p
ending
commit
|
commitdiff
|
tree
2013-04-29
Carsten Kutzner
Evaluate enforced rota
t
ion
p
otenial with Ve
r
let, f
i
xes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten Kutzner
Esse
n
tial dynamics: fixed
l
egend
i
n ED
.
x
v
g ou
t
put
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzner
Made g_tune_pme work wit
h
4
.
6
i
f user sets
"-p"
c
ommand
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten Kutzner
Fixed the MPI recogni
t
ion
string in g_tune_
p
me
commit
|
commitdiff
|
tree
2013-01-22
Carsten Ku
t
zne
r
Moved a few comme
n
t
s bac
k
into position
commit
|
commitdiff
|
tree
2013-01-17
Ca
r
sten
K
utzner
A
d
d
ed note abou
t
make_edi
a
nd floodi
n
g in
E
D par
a
graph
commit
|
commitdiff
|
tree
2013-01-16
Carsten Ku
t
zner
Ma
d
e g
_
tune_pme
w
o
r
k correc
t
ly
again
w
i
th th
r
e
a
d-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten Kutzner
Essential dynamics output file now in
.
xvg f
o
rmat
commit
|
commitdiff
|
tree
2012-12-20
Carste
n
Ku
t
zner
Small fix for
g_tune_pme
commit
|
commitdiff
|
tree
2012-12-20
C
a
rsten Kutzner
Essential dynamics: fixed res
t
arts when E
D
g
roup
ha
s
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carst
e
n Kutz
n
e
r
Mad
e
g
_
tune_pme wo
r
k correctly
w
hen ir-
>
init_step
> 0
commit
|
commitdiff
|
tree
2012-10-16
Ca
r
s
t
en Kutzn
e
r
Made g_tun
e
_pme read (n
s
/day) fr
o
m 4
.
6 m
d
.
log output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
R
e
moved
obsolete hint in error m
e
ssage
.
commit
|
commitdiff
|
tree
2012-08-07
Cars
t
en Ku
t
z
ner
Fi
x
ed esse
n
t
ial dynami
c
s
/ flood
i
ng group
PBC
s
e
r
i
al
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kutzner
Fixed calcula
t
ion
o
f
p
ro
j
ection
f
or STAR
an
d
/o
r
SOR
I
commit
|
commitdiff
|
tree
2012-08-06
C
a
rst
e
n K
u
tzner
A
d
ded commen
t
in get_structure
a
bout which
str
u
ctures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Cars
t
en Kutzner
Fixe
d
segv in essential dynamics module
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kutzner
Enforced
r
ota
t
ion:
P
B
C
/
r
e
start fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten K
u
t
z
ne
r
Sma
l
l
f
ix for g
_
tune_pme
commit
|
commitdiff
|
tree
2012-05-23
Cars
t
en
Ku
t
zner
Revised
g
_
tun
e
_pme
commit
|
commitdiff
|
tree
2012-03-09
Ca
r
sten Kutz
n
er
Mer
g
e "Impr
o
ve
d
w
arni
n
g
note w
i
th
D
D a
n
d peri
o
dic molecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
C
a
rste
n
Ku
t
zner
New tool that extrac
t
s
dye d
y
nami
c
s
f
rom
t
rajectories
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutzner
Added -dhdl to t
p
r file l
i
s
t, fixes #855
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kutzner
En
f
orced rotation
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutzner
Ac
t
u
a
lly -
c
pi and
-bcpo must n
o
t
be id
e
n
t
ical
commit
|
commitdiff
|
tree
2011-10-31
C
arsten Kutzner
Fixed bug #830 (se
g
v in
d
o_ds
s
p)
commit
|
commitdiff
|
tree
2011-08-31
Ca
r
s
t
en Kutzner
Re
m
ove
s
egv in xpm
2
ps, fixes #611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kutzner
Re
m
ov
e
segv in
x
pm
2
p
s, fixes
#
611
commit
|
commitdiff
|
tree
2011-08-25
Carsten K
u
tzne
r
Instea
d
of a segv, md
r
un now gives an e
r
ror
m
sg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
C
a
r
s
ten
K
utzner
Typo
.
commit
|
commitdiff
|
tree
2011-07-29
Ca
r
sten Kutzner
Fixed calcu
l
ation of max
and min nu
m
ber o
f
PME
-
only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carst
e
n K
u
tzner
Removed
old-
f
ashione
d
MPE
logging code
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kut
z
ner
Add
e
d two missing headers
commit
|
commitdiff
|
tree
2011-07-06
C
arsten Kutzne
r
Add
e
d globsi
g
.
h to include/ty
p
es/Ma
k
efi
l
e
.
am
commit
|
commitdiff
|
tree
2011-05-30
Ca
r
sten Kutz
n
er
Flooding as harm
.
restraint: Abort
w
hen orig
i
n
p
osition
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Che
c
ks for zero-mass atoms
in ED, bette
r
o
rder
i
ng of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten Kutzne
r
Fixed wron
g
e
r
r
o
r message when us
i
ng floodin
g
code
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Ca
r
sten
K
u
tzn
e
r
F
ixed bu
g
#714:
dep
r
ecated structure
i
n g
e
tt
i
meofd
a
y
commit
|
commitdiff
|
tree
2011-02-25
Cars
t
en Kutzner
Cor
r
ected
o
utput of a warning message
.
commit
|
commitdiff
|
tree
2011-02-25
Carst
e
n K
u
tzner
Added the -f
i
x optio
n
to
g
_tu
n
e_pm
e
for tuning o
f
rcoulomb
.
.
.
commit
|
commitdiff
|
tree
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