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Make gmx_multisim_t a C++ object
2019-04-04
Carsten Kutzner
Early exi
t
from mdrun if group scheme is d
e
tected in
.
.
.
commit
|
commitdiff
|
tree
2018-05-10
Carsten
Kutzner
In
t
roduce helper
classes for force provider input and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carsten Ku
t
zner
F
ix
a few typo
s
in SIMD documentati
o
n
commit
|
commitdiff
|
tree
2017-12-20
C
a
rsten Kutz
n
er
Des
t
r
u
ct
MD
M
odules/force provider
s
prior t
o
calling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
Carsten
K
utzner
F
ix electric
f
i
e
ld
.
mdp
docum
e
nta
t
ion
commit
|
commitdiff
|
tree
2017-08-10
C
arsten
Kutzner
C
o
rrected the PDF
manual
t
o r
e
flect that al
l
to
o
ls
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
C
arsten Kutzner
A
d
d
ed miss
i
ng
.
mdp file d
o
cumentat
i
on for
t
h
e
enforced
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten
K
utzner
Added miss
i
ng
.
mdp file
do
c
um
e
ntation for the enforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carsten Kutzner
Fixed #2206 IMD in
t
erface malfunctions
commit
|
commitdiff
|
tree
2017-06-16
C
a
rs
t
en Kutzner
F
ixed
a
consisten
c
y
check in make_edi for flooding
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutzner
Moved
essential dynamics initialization
c
all into
d
o_md
(
)
commit
|
commitdiff
|
tree
2017-06-09
Carsten K
u
t
z
ner
Adopt and d
o
cument implementation policy for MD modules
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kutzner
Minor he
a
der file cleanu
p
in ED,
I
MD and
C
o
m
pEL module
s
commit
|
commitdiff
|
tree
2017-04-19
Carst
e
n
Kutzner
R
e
m
ove un
u
se
d
forward declarati
o
n
s
of t_c
o
mmre
c
i
n
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Carsten Kutzne
r
Remove u
n
n
e
cessary incl
u
de
commit
|
commitdiff
|
tree
2016-11-16
C
a
rsten Kut
z
ner
In
c
reased the
default
reset st
e
p to 1
5
00 in gmx tune_pme
commit
|
commitdiff
|
tree
2016-11-15
Car
s
ten Kutzner
Fi
x
ed ty
p
o
i
n
membed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Cars
t
en Kutzn
e
r
Correct
e
d value
o
f
electric conversion fa
c
tor f
in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
Clean-
u
p c
o
de
f
or swa
p
coords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten K
u
tzner
Clarified l
i
cense text in the
.
tex manua
l
commit
|
commitdiff
|
tree
2016-03-17
Ca
r
sten K
u
tzner
Fix me
m
b
ed initial
i
zation
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutzner
Sm
a
l
l
u
p
d
ate t
o
refer
e
nce m
a
nual
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzn
e
r
C
han
g
ed norm(
.
.
.
) > 0
condition to norm2(
.
.
.
) > 0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Cars
t
en Kut
z
ner
Improv
e
d/enlarged Fig
.
4
.
9 in manual for bett
e
r reada
b
il
i
ty
commit
|
commitdiff
|
tree
2016-01-20
C
arst
e
n Ku
t
zner
Ma
d
e g_tune_pm
e
work with -cpi -
d
ef
f
n
m
combination
commit
|
commitdiff
|
tree
2015-11-17
Ca
r
sten Kutzner
Fixed -npstring command line
argument in gm
x
tune_pme
commit
|
commitdiff
|
tree
2015-11-13
C
arsten Kutzn
e
r
I
o
n/wa
t
er position swapping for mu
l
tiple ion type
s
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutzn
e
r
Descri
b
ed
t
he
c
omp
u
tat
i
onal
e
lectrophy
s
iology
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
E
xtra option
s
for
c
ompu
t
a
t
ional elec
t
rophysiology
.
commit
|
commitdiff
|
tree
2015-10-07
C
arsten Kutzner
Code cleanup
i
n
sw
a
pcoor
d
s
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Carsten Ku
t
zn
e
r
Fixed a bug in comp
u
tati
o
nal electrophysi
o
logy w
i
t
h DD
commit
|
commitdiff
|
tree
2015-07-15
Carsten Kutzn
e
r
R
e
mov
e
d informa
t
ion about
o
bso
l
ete
.
edo file forma
t
commit
|
commitdiff
|
tree
2014-12-09
Ca
r
sten Kutzn
e
r
M
a
k
e tune_pme understa
n
d the "-nsteps" option
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten
K
u
tzner
Fixed a typo in the manual
.
commit
|
commitdiff
|
tree
2014-11-12
Carste
n
K
u
tz
n
e
r
Updated s
o
me
.
mdp file variables to use "-"
i
nstead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
C
a
r
s
ten Kutzner
Fix or
d
er of ED/swap blocks during checkpoin
t
reading
.
commit
|
commitdiff
|
tree
2014-10-01
C
a
r
s
t
en Kutzne
r
A
l
low g
m
x
t
une_pme t
o
skip th
e
check
for c
o
mman
d
-line
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Cars
t
en
Kut
z
ner
Fixed output of
eigen
v
a
l
ues in g_covar
.
F
i
xes #15
7
5
commit
|
commitdiff
|
tree
2014-06-27
Cars
t
en Kutzner
Re
m
o
ve obs
o
lete pull-g
e
o
metry option 'pos
i
tion
'
f
r
om
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten Kutz
n
er
Re-use g
m
x
_wit
h
in_tol from math/uti
l
ities inste
a
d
of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Cars
t
e
n
Ku
t
zner
Fix documentation of swap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten K
u
t
z
ner
Fix docum
e
ntation issue
s
fo
r
intera
c
tive MD
module
.
commit
|
commitdiff
|
tree
2014-03-26
C
a
rsten Kutz
n
er
D
o
cum
e
ntation hous
e
-keeping in fi
l
e swapcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
C
a
rsten Kutz
n
e
r
A
void cross
product with zero vector in
r
otational
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Car
s
ten K
u
tzne
r
The van der Waals
r
a
dius mu
s
t equal the Coulomb
r
adius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
S
m
a
ll enhancement of
computational
e
lectrophys
i
ology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
C
a
rsten
K
utzner
A
l
l
o
w for "computational electrophysiology" simulations
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten Kutzner
M
o
ve pu
l
l code to separa
t
e subdirectory
commit
|
commitdiff
|
tree
2014-01-11
Carsten Kutzner
Move ess
e
n
t
ial dynamics / flooding code to separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Cars
t
en Kutzn
e
r
Read e
s
sential dynamics data f
r
o
m
checkpoint at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzn
e
r
Rem
o
ved a few typos
in
three German quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Ca
r
s
t
en
K
utzner
Pass o
n
default value of radste
p
i
n m
a
k
e
_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten
Kutz
n
er
Essent
i
al
d
ynamics:
m
ove
b
NeedDoE
d
sam evaluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Carsten K
u
tzner
Fixed ess
e
nti
a
l dynamics (E
D
) continuation from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Carsten Kutzner
Properly finalize MPI on mdrun -versi
o
n
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-06-26
Carsten
Kutzner
Fixed -npstring comm
a
n
d
li
n
e
argu
m
ent
in g_tune_p
m
e
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
Fixed calcul
a
tion o
f
sl
a
b buffe
r
size fo
r
fl
e
x
i
ble
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Ca
r
s
ten Kutz
n
e
r
F
ix
f
or a rar
e
condition in fl
e
xib
l
e
rotat
i
on
p
otentials
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten Kutzne
r
Cod
e
cleanup
in
e
nforced rotat
i
on modu
l
e,
r
em
o
ve warnings
.
commit
|
commitdiff
|
tree
2013-05-16
Ca
r
s
t
en Kutzner
C
h
o
o
se the
PBC image
o
f each ro
t
ation g
r
oup a
t
om
d
ep
e
nding
commit
|
commitdiff
|
tree
2013-04-29
Carsten Ku
t
zner
Evalua
t
e
enforced rotation potenial
w
ith V
e
rlet, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten Kutzner
Essen
t
ial dynamics:
f
i
xe
d
legen
d
in E
D
.
xvg
o
utput
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Ca
r
sten
Kutzner
Made g_tune_pm
e
work w
i
t
h 4
.
6
if user
s
ets "-p"
command
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten Kutzner
Fixed the MPI recognition st
r
i
ng in g_t
u
ne_pme
commit
|
commitdiff
|
tree
2013-01-22
Carsten Kutz
n
er
Mo
v
ed a few co
m
ment
s
ba
c
k int
o
position
commit
|
commitdiff
|
tree
2013-01-17
Carsten
Kutzner
Ad
d
ed note
a
bout m
a
ke_edi and fl
o
oding in ED paragraph
commit
|
commitdiff
|
tree
2013-01-16
Carsten Kutzner
Made g_tune_pme
w
o
r
k c
o
rrectly
ag
a
in w
i
th thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carst
e
n Kutzner
Es
s
ential dynamics output file now in
.
xvg for
m
at
commit
|
commitdiff
|
tree
2012-12-20
Carsten K
u
tzner
Small fix f
o
r g_tune_pme
commit
|
commitdiff
|
tree
2012-12-20
C
a
r
sten Kut
z
ner
Essenti
a
l dynamics: fixed resta
r
ts when E
D
g
roup
h
as
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carste
n
Kutzner
Made
g_t
u
ne_pme work cor
r
e
ctl
y
w
hen i
r
->init
_
s
t
ep
>
0
commit
|
commitdiff
|
tree
2012-10-16
Carst
e
n Ku
t
zne
r
Mad
e
g_tune_pme rea
d
(ns/day) from
4
.
6 md
.
log out
p
ut
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzn
e
r
Removed obsolete hint
in erro
r
message
.
commit
|
commitdiff
|
tree
2012-08-07
C
arsten Kutzner
Fixed e
s
sential
d
y
namics / floodin
g
group PBC
s
erial
commit
|
commitdiff
|
tree
2012-08-06
Carsten
K
u
t
z
ne
r
Fixed calculation of projection for STAR
a
nd/or
SORI
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kutzne
r
Added comment in get_structure about whi
c
h
s
tructures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutz
n
er
Fi
x
e
d
segv
i
n
essentia
l
d
y
n
a
mics mod
u
le
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kutzner
Enforced rotation: PBC/restart fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Kut
z
ner
Small fix
for g_
t
une
_
pme
commit
|
commitdiff
|
tree
2012-05-23
Carsten Kutzner
Revis
e
d g_
t
une_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten
Kutzner
Merge "Impro
v
e
d warn
i
ng
n
ote with
D
D and pe
r
iodic mo
l
ecu
l
es
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten Kutzner
New t
o
ol that
ext
r
acts
dye dynamics from t
r
aject
o
r
ies
commit
|
commitdiff
|
tree
2011-12-20
C
a
r
s
ten Kutzner
Add
e
d -dhdl
t
o tpr f
i
le list, fixes #8
5
5
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kutzner
Enforced ro
t
atio
n
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutzner
A
ctually -c
p
i
and -bcpo must not
b
e i
d
entica
l
commit
|
commitdiff
|
tree
2011-10-31
Carsten Kutzn
e
r
F
ix
e
d bug #83
0
(s
e
gv
in
do_
d
ssp)
commit
|
commitdiff
|
tree
2011-08-31
Ca
r
sten Kutzner
Remove segv in xpm2ps
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kutzn
e
r
Remove segv
in
xpm2ps
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-25
Ca
r
s
t
en Kutz
n
e
r
Instead
o
f a seg
v
, mdrun now gives an
e
rror m
s
g if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Car
s
ten Kut
z
ner
T
y
p
o
.
commit
|
commitdiff
|
tree
2011-07-29
Cars
t
en Kutzner
Fixed ca
l
c
u
lati
o
n of max and
mi
n
number of PME-o
n
ly
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutz
n
er
Removed old-fashione
d
MPE logg
i
ng
c
ode
commit
|
commitdiff
|
tree
2011-07-11
Carsten K
u
tzner
Added two
missing head
e
rs
commit
|
commitdiff
|
tree
2011-07-06
C
a
r
ste
n
Kutzner
Added g
l
obsig
.
h to in
c
lude/types/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Ku
t
zner
Floodi
n
g as h
a
rm
.
restrai
n
t: Abort when origin po
s
ition
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Checks for zero-mass atoms in ED, better order
i
ng of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten Kut
z
ner
Fixed wrong err
o
r
m
es
s
age when using fl
o
oding co
d
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Carsten Kutzner
F
ixed b
u
g #
7
1
4
: deprecated structure in gettimeofday
commit
|
commitdiff
|
tree
2011-02-25
C
arsten Kut
z
ner
Corrected output of a warning me
s
sage
.
commit
|
commitdiff
|
tree
2011-02-25
Carsten K
u
tzner
Added the -f
i
x op
t
ion to
g
_tu
n
e
_
p
m
e for tunin
g
of rcoulomb
.
.
.
commit
|
commitdiff
|
tree
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