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Fixed bug in orires code that was checking too strict.
2019-10-02
Carsten Kutzner
Update the www link to the Dox
y
g
en doc
u
men
t
ation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Carsten Ku
t
z
n
er
Update the ww
w
link to the Doxygen documentati
o
n in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
C
arsten
K
utzner
Mo
v
e For
c
eProvid
e
rs
c
la
s
s into the gmx name
s
pace
commit
|
commitdiff
|
tree
2019-09-30
Carst
e
n Ku
t
zner
Corrected
a
f
ew
t
ypos in d
o
cumentati
o
n and comment
s
commit
|
commitdiff
|
tree
2019-04-04
Carsten Kutzn
e
r
Ea
r
ly exit from md
r
un i
f
group scheme is detected in
.
.
.
commit
|
commitdiff
|
tree
2018-05-10
C
a
rsten
K
utzner
Int
r
oduce helpe
r
classes for f
o
r
ce pro
v
ider
i
npu
t
and
.
.
.
commit
|
commitdiff
|
tree
2018-01-08
Carsten
K
utzner
Fix a few ty
p
os i
n
SIMD doc
u
men
t
ation
commit
|
commitdiff
|
tree
2017-12-20
Carsten
K
utzner
Destr
u
ct MDModules/forc
e
prov
i
d
ers prior to
callin
g
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
Carsten Ku
t
zner
Fix
e
l
ec
t
ric field
.
mdp documentation
commit
|
commitdiff
|
tree
2017-08-10
Cars
t
e
n Kutzner
Correct
e
d the PDF manual
t
o re
f
lect that all tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten Ku
t
zner
Added mis
s
ing
.
mdp file documentation for the
e
n
forced
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten
Kutz
n
er
Add
e
d missing
.
mdp file
d
ocumentation for the enforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Ca
r
s
t
en Kutzner
Fixed
#2
2
06 IMD inter
f
ace m
a
lfunctions
commit
|
commitdiff
|
tree
2017-06-16
Carste
n
Ku
t
zne
r
Fixed a c
o
nsistency check in make_edi for flooding
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutzner
Moved es
s
ential dynamics initialization call into
d
o_md
(
)
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutzner
A
dopt a
n
d do
c
ument
i
mpl
e
ment
a
ti
o
n policy for MD modules
commit
|
commitdiff
|
tree
2017-04-29
Cars
t
en K
u
tzner
Minor
header file cleanup in
E
D, IMD an
d
CompEL module
s
commit
|
commitdiff
|
tree
2017-04-19
Carsten Kut
z
ne
r
R
e
move u
n
used fo
r
ward de
c
larations of t_commr
e
c in
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Ca
r
sten Kutzner
R
e
mov
e
unnecessary incl
u
de
commit
|
commitdiff
|
tree
2016-11-16
C
ar
s
ten Kutzne
r
Incre
a
se
d
the defaul
t
reset
s
tep to 1500 in gmx tune_p
m
e
commit
|
commitdiff
|
tree
2016-11-15
C
arsten Kutzner
Fixed typo
i
n membed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Cars
t
e
n K
u
tzner
Co
r
rected value
o
f
e
lectric conversion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
Cle
a
n-up code
for sw
a
p
coords
.
commit
|
commitdiff
|
tree
2016-03-18
C
arste
n
Kutzner
Clarified licen
s
e
text i
n
the
.
te
x
manual
commit
|
commitdiff
|
tree
2016-03-17
Carsten Kutzner
Fix
m
e
m
bed
ini
t
ia
l
iz
a
tion
commit
|
commitdiff
|
tree
2016-02-18
Ca
r
sten Kutzn
e
r
Small up
d
at
e
to refere
n
ce m
a
n
u
a
l
commit
|
commitdiff
|
tree
2016-02-16
Carste
n
Kutzner
Ch
a
nged no
r
m
(
.
.
.
) > 0 condition to norm2(
.
.
.
) >
0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten
Kut
z
ner
I
m
pr
o
ve
d
/enlarged Fig
.
4
.
9 in manual fo
r
better readability
commit
|
commitdiff
|
tree
2016-01-20
Cars
t
e
n
Kutzner
Ma
d
e g_tune_pme work wi
t
h
-
cpi -de
f
f
nm c
o
mbin
a
tion
commit
|
commitdiff
|
tree
2015-11-17
Carst
e
n
Ku
t
zner
Fixed -npst
r
ing
c
om
m
an
d
li
n
e argu
m
ent in gmx t
u
ne_
p
me
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzner
Ion
/
water position
s
wappin
g
for mult
i
ple ion types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kut
z
n
er
Desc
r
ibed the
c
o
mputational el
e
ctroph
y
s
iology
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Extra option
s
for computational e
l
ect
r
ophysiolo
g
y
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Code clean
u
p i
n
swapcoords
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Car
s
ten Kutzne
r
Fixed a bug in computational elect
r
o
physiolo
g
y
w
i
th
D
D
commit
|
commitdiff
|
tree
2015-07-15
Ca
r
sten Kutzner
Removed
information
a
bout obs
o
lete
.
e
do file
format
commit
|
commitdiff
|
tree
2014-12-09
Carste
n
Kutzner
Ma
k
e tune_pme unde
r
s
t
and the
"
-
nsteps" optio
n
.
Fi
x
es
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Cars
t
en
K
utzner
Fixe
d
a
t
y
po
i
n the manual
.
commit
|
commitdiff
|
tree
2014-11-12
Carsten Kutzner
U
p
d
a
ted some
.
mdp file
v
ariables to use "-"
i
nstead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carsten Kutzner
Fix order o
f
E
D
/swap blocks du
r
ing checkpoint r
e
ading
.
commit
|
commitdiff
|
tree
2014-10-01
C
a
rsten
K
u
tzne
r
Allow gmx tune_p
m
e
t
o
skip
t
he check for comma
n
d-li
n
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
C
ar
s
ten Kutzne
r
F
i
x
ed output of eigenval
u
es in g_covar
.
Fixes
#
1
575
commit
|
commitdiff
|
tree
2014-06-27
C
a
rsten Kutzn
e
r
R
e
move
o
b
sole
t
e pull-geometry
optio
n
'position' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten Kutz
n
er
Re-use gmx_within_to
l
from
m
ath/utilities instead o
f
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carste
n
Kutzner
Fix documentation of swap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carsten
K
utzner
Fix documentation issu
e
s for inte
r
active MD
m
odule
.
commit
|
commitdiff
|
tree
2014-03-26
Car
s
ten K
u
t
zner
D
ocu
m
entation house-keeping
in file s
w
apcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
Cars
t
en Kutzner
Avoi
d
cross product
with z
e
ro
v
ect
o
r in rotationa
l
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
C
arsten Kutzner
The van der Waa
l
s radius mu
s
t equal the Coulomb radiu
s
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carst
e
n Kutzner
Sma
l
l enhancement of
computational electrophysiology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten K
u
tzn
e
r
Allow for "computational
e
lectrophysiolog
y
" si
m
ul
a
tions
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten K
u
t
zner
Move
pull code to sepa
r
ate
subdirecto
r
y
commit
|
commitdiff
|
tree
2014-01-11
Carsten
K
utz
n
er
Move essential
dyn
a
mics / floodin
g
c
o
de t
o
separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten Kutzner
Read essenti
a
l dynamic
s
data
f
rom check
p
o
in
t
at c
o
rrect
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
Removed
a
few typos in
t
h
ree Ge
r
man qu
o
tes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten
Kutzner
P
ass on default value of radste
p
i
n ma
k
e
_
e
d
i
commit
|
commitdiff
|
tree
2013-12-25
Carsten Kutzne
r
Essential dynamics: move
bNeedDoE
d
sam evaluation
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Carsten Kutzner
Fixed essential dyna
m
ics (ED) continuati
o
n from
.
c
p
t
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
C
a
r
sten Kutzne
r
Properly finalize MPI on m
d
r
un -version
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-06-26
Carsten Ku
t
zner
Fixed -npstri
n
g c
o
mmand line argument in g
_
t
une_pme
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzn
e
r
Fixed
c
al
c
ulatio
n
of sl
a
b buff
e
r
s
ize f
o
r fle
x
ible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Car
s
t
en Kutzner
Fix for a rare
c
ondition
i
n
flexible rotatio
n
pote
n
tials
.
commit
|
commitdiff
|
tree
2013-05-27
C
arsten K
u
t
z
ner
C
ode
cleanup
in enforced
r
otation m
o
dule
,
r
emove war
n
ings
.
commit
|
commitdiff
|
tree
2013-05-16
C
a
rsten Kutzner
Choose t
h
e PBC image of each rotat
i
on
g
roup atom
d
e
pending
commit
|
commitdiff
|
tree
2013-04-29
C
a
rsten
K
utzner
Eval
u
ate enforced rotation
p
ot
e
nial with
Verlet, fixe
s
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Cars
t
e
n Kutzne
r
Essential
dynami
c
s: fix
e
d
l
eg
e
nd
in ED
.
x
vg out
p
ut
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
C
a
rsten Kutzner
Made g_tune_pme work wit
h
4
.
6 if user se
t
s "-p" com
m
and
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
a
rsten Kut
z
n
er
Fixed the MPI re
c
ognition string in g_tun
e
_pme
commit
|
commitdiff
|
tree
2013-01-22
Carsten Ku
t
zner
M
o
ved a
f
ew
comments b
a
ck into position
commit
|
commitdiff
|
tree
2013-01-17
Carst
e
n K
u
tz
n
er
Ad
d
ed note about make_edi and flooding
i
n ED pa
r
agraph
commit
|
commitdiff
|
tree
2013-01-16
C
arsten Kutzner
M
a
de g_
t
une_p
m
e work
c
orre
c
tly
a
gai
n
wit
h
thre
a
d-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten
Kutzner
Essential dynamic
s
outpu
t
file now in
.
x
vg format
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzn
e
r
Small fix for g_
t
une_pme
commit
|
commitdiff
|
tree
2012-12-20
Carsten
Kutz
n
er
Essential
dynami
c
s: fixed restarts when
E
D
group h
a
s
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Car
s
ten Kutzner
Made g_tun
e
_pm
e
work co
r
rec
t
ly whe
n
ir->init_step > 0
commit
|
commitdiff
|
tree
2012-10-16
Cars
t
e
n Kutz
n
er
Made
g
_tune_
p
me r
e
ad (ns
/
day)
fr
o
m 4
.
6 md
.
log
o
utput
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutz
n
e
r
Rem
o
v
ed obso
l
ete hint in er
r
or message
.
commit
|
commitdiff
|
tree
2012-08-07
Carst
e
n Kutzner
F
ixed essentia
l
dynamics /
flood
i
ng group P
B
C
s
erial
commit
|
commitdiff
|
tree
2012-08-06
Carsten
K
utzner
Fi
x
ed calcula
t
ion of projectio
n
f
or
S
TAR and/or S
O
R
I
commit
|
commitdiff
|
tree
2012-08-06
Carsten
K
utz
n
er
Added comm
e
n
t
in
get_s
t
ructure about
w
hich structures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carst
e
n Kutz
n
er
Fixed se
g
v in ess
e
ntial dynamics module
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kutzner
Enforced
rotation: PBC/re
s
tart fix
commit
|
commitdiff
|
tree
2012-06-11
Car
s
ten
Kutzn
e
r
Sma
l
l fix fo
r
g
_tu
n
e_
p
me
commit
|
commitdiff
|
tree
2012-05-23
Carsten Kutzner
Revise
d
g_tune
_
pm
e
commit
|
commitdiff
|
tree
2012-03-09
C
a
rsten K
u
tzner
M
e
rge "Improved warning
n
ote
with DD and p
e
riod
i
c
molecul
e
s
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten Ku
t
zne
r
New to
o
l that extracts dye dyna
m
ic
s
from tr
a
j
e
ctories
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutzner
Added -dhdl to tpr file list, fix
e
s #855
commit
|
commitdiff
|
tree
2011-12-19
Carste
n
Kutzn
e
r
Enforced rotat
i
on
commit
|
commitdiff
|
tree
2011-11-22
Cars
t
e
n
Kutzner
Actually
-cpi a
n
d
-
bcpo mu
s
t not be ide
n
tic
a
l
commit
|
commitdiff
|
tree
2011-10-31
C
a
rsten Kutzner
F
i
xed
bu
g
#8
3
0
(
segv in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Carsten K
u
tzn
e
r
Remo
v
e seg
v
in xp
m
2ps, fix
e
s
#611
commit
|
commitdiff
|
tree
2011-08-26
Cars
t
en Kutzner
Rem
o
ve segv
i
n xpm2p
s
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-25
Carsten Kutzner
Inst
e
ad
of a se
g
v,
mdrun now gives an er
r
o
r
msg
i
f
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
C
arst
e
n
Kutzner
T
ypo
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten
Kutzner
Fixed
c
alculati
o
n
o
f
m
a
x
and m
i
n numbe
r
of PME
-
only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carst
e
n
K
u
t
zner
R
e
m
o
ved o
l
d-fa
s
hione
d
MPE loggi
n
g
c
ode
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutzner
A
d
ded two
m
i
ssing h
e
aders
commit
|
commitdiff
|
tree
2011-07-06
Carsten Kutzner
Added globsig
.
h to inclu
d
e/types/Makefi
l
e
.
a
m
commit
|
commitdiff
|
tree
2011-05-30
Carste
n
Kutzner
Floodi
n
g as
h
arm
.
r
e
straint: Abor
t
when origin positio
n
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Che
c
ks for
z
e
r
o-mass a
t
oms in ED, better ordering of
.
.
.
commit
|
commitdiff
|
tree
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