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Updates to documentation
2016-04-14
Carsten Ku
t
z
n
e
r
Corrected va
l
ue of ele
c
tric conver
s
ion fact
o
r
f
in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carst
e
n K
u
tzne
r
Cle
a
n-up code for swapcoords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten Kutzner
Clarifi
e
d licens
e
text in t
h
e
.
tex
manual
commit
|
commitdiff
|
tree
2016-03-17
Carsten Kut
z
ner
Fix me
m
bed initialization
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutz
n
er
Smal
l
update
t
o
r
efe
r
ence manual
commit
|
commitdiff
|
tree
2016-02-16
C
a
rsten Kutzner
Cha
n
g
e
d norm(
.
.
.
) > 0 co
n
dition to norm2(
.
.
.
) >
0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carst
e
n Kutzne
r
Impr
o
ved/enlar
g
ed Fig
.
4
.
9 in man
u
al for better readab
i
lity
commit
|
commitdiff
|
tree
2016-01-20
Carste
n
Kutzner
Made g
_
tun
e
_pme work
with -cpi -deffnm combination
commit
|
commitdiff
|
tree
2015-11-17
Carsten Kutzner
Fixed -npstrin
g
c
ommand line
ar
g
ument
i
n gmx tune_pme
commit
|
commitdiff
|
tree
2015-11-13
Carst
e
n Kutzner
Ion/wa
t
er
p
osition swapp
i
n
g
for
m
ult
i
ple
io
n
types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
C
a
r
sten Kutzn
e
r
D
e
scribed the com
p
utat
i
onal electroph
y
siolog
y
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Car
s
ten K
u
tzner
Extra
o
ptions for
c
omput
a
ti
o
nal e
l
ectrophy
s
i
ology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
C
o
de cleanup in swap
c
oor
d
s
.
c
p
p
commit
|
commitdiff
|
tree
2015-10-02
Carsten
Kutzner
Fix
e
d
a
bug
i
n
co
m
puta
t
ional electr
o
physiology wi
t
h DD
commit
|
commitdiff
|
tree
2015-07-15
Carsten Kutzner
Remov
e
d information about obsolete
.
edo fil
e
format
commit
|
commitdiff
|
tree
2014-12-09
Ca
r
sten
K
ut
z
ner
Make tun
e
_pme understand the
"
-nsteps"
opti
o
n
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten Kutzner
Fixed a
t
y
p
o in the
manual
.
commit
|
commitdiff
|
tree
2014-11-12
Carste
n
Kutzner
Up
d
a
t
ed so
m
e
.
mdp file variables
t
o use "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carsten Kutzner
Fix
o
rder of ED/swap blocks during checkpoin
t
readin
g
.
commit
|
commitdiff
|
tree
2014-10-01
Carsten Kut
z
ner
Allow gm
x
tune_pme to skip the chec
k
for command-line
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Ca
r
sten K
u
t
zner
Fixed o
u
tput of eigenvalues in g
_
covar
.
Fixes #1
5
75
commit
|
commitdiff
|
tree
2014-06-27
Ca
r
sten
K
utzner
Remove o
b
solete pull
-
geometry option 'position'
f
r
om
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten Kutzner
Re-use gmx
_
with
i
n_tol from math/ut
i
lities
i
nstead
o
f
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Car
s
ten Kutzner
Fix documentation of swap/enums
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carste
n
Ku
t
zner
F
i
x
documen
t
ation is
s
u
es for i
n
teractive MD modu
l
e
.
commit
|
commitdiff
|
tree
2014-03-26
Ca
r
sten K
u
t
z
ner
Do
c
umen
t
ation
h
ouse
-
keeping i
n
file swapcoords
.
c
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kutzner
Avoid
c
ross produc
t
w
i
th
zero vector
in rotatio
n
a
l
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carste
n
Ku
t
zner
Th
e
van der Waals radius must
eq
u
al the
C
o
ulomb radius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
Small
e
n
h
a
n
cement of
c
om
p
utational electrophy
s
io
l
ogy
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
Carsten Kutzner
Allow for "computatio
n
al el
e
ctrophysiolo
g
y" simulations
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carsten
K
utzner
Move pull code to s
e
parate subdirectory
commit
|
commitdiff
|
tree
2014-01-11
Carsten
Kutzner
Move e
s
sential dynamics /
f
looding code
t
o
sep
a
r
a
te
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Carsten
K
utzner
Read essent
i
al dynamics data from checkpoint at corr
e
c
t
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
Remove
d
a few typos in
t
hree German quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten Ku
t
zner
P
a
ss
o
n
default
v
alue
o
f radstep in mak
e
_edi
commit
|
commitdiff
|
tree
2013-12-25
C
a
rsten Kutzner
Essential dyn
a
mics: mo
v
e
bNee
d
DoEd
s
am evaluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Cars
t
en Kutzner
Fixed
e
ssential dynamic
s
(ED) continuation from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Ca
r
sten K
u
t
z
ner
P
r
operly fi
n
aliz
e
MPI o
n
mdrun -
v
er
s
ion
.
Fixes #131
3
commit
|
commitdiff
|
tree
2013-06-26
Cars
t
e
n
Kutz
n
er
F
i
xed -npstring command line ar
g
umen
t
in g_tune_pm
e
commit
|
commitdiff
|
tree
2013-05-28
Carst
e
n
Kutzner
Fixed calculation of slab
b
uffe
r
size for flexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Car
s
ten K
u
tzner
Fix for a rare
condition in flexible ro
t
a
t
ion potentials
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten Kut
z
ner
Code cleanup in enforce
d
rotation module,
remove warn
i
n
gs
.
commit
|
commitdiff
|
tree
2013-05-16
Carsten Kutz
n
e
r
Choose the P
B
C
image of each
r
otation group atom depending
commit
|
commitdiff
|
tree
2013-04-29
C
ar
s
t
en Kutzner
Ev
a
luate enfor
c
ed rota
t
ion potenial with V
e
rlet
,
fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten K
u
tzner
Essential dynamic
s
: fixed legend
i
n
ED
.
x
v
g
o
utput
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzner
Made g_
t
u
ne_pme
work
with 4
.
6
if
u
s
e
r sets
"
-p" comma
n
d
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten
Kut
z
ner
Fixed the MP
I
recog
n
itio
n
s
t
ri
n
g in g_tu
n
e_pme
commit
|
commitdiff
|
tree
2013-01-22
Car
s
ten Kut
z
ne
r
Mov
e
d a few comme
n
t
s
back int
o
posi
t
i
o
n
commit
|
commitdiff
|
tree
2013-01-17
C
a
r
s
ten
Kut
z
ner
A
dded note ab
o
ut make_edi and f
l
ooding in ED paragraph
commit
|
commitdiff
|
tree
2013-01-16
Ca
r
sten Ku
t
z
n
er
Made g_tune_pme
w
o
r
k
corr
e
ctly agai
n
w
ith thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten Kutzner
E
ss
e
ntial dynamics output file now
i
n
.
xvg fo
r
mat
commit
|
commitdiff
|
tree
2012-12-20
Carst
e
n Kutz
n
er
Sma
l
l
fix for
g_tune_pm
e
commit
|
commitdiff
|
tree
2012-12-20
Carsten Kutzner
E
s
sential dynamic
s
:
f
ixed
r
estarts when ED grou
p
has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kutzn
e
r
Made g_tune_p
m
e
work correctly when ir->init_step > 0
commit
|
commitdiff
|
tree
2012-10-16
Carsten Ku
t
zner
Made g_tun
e
_pme
read (ns/day) from 4
.
6 md
.
l
og output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
Rem
o
ved obsolet
e
hint
i
n err
o
r message
.
commit
|
commitdiff
|
tree
2012-08-07
Carst
e
n
Kutzner
Fi
x
e
d
essential
d
ynamics
/
flooding grou
p
P
B
C serial
commit
|
commitdiff
|
tree
2012-08-06
Ca
r
sten Kutzner
Fixed calcul
a
tion o
f
p
rojection fo
r
STAR and/or SORI
commit
|
commitdiff
|
tree
2012-08-06
Carste
n
Kut
z
ner
Added
c
omment in get_structure ab
o
ut wh
i
ch
s
t
ruct
u
res
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carst
e
n Kutzner
F
i
x
ed segv
in essential
dynamics mo
d
ule
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kutzner
Enforced r
o
tation: PBC/restart fix
commit
|
commitdiff
|
tree
2012-06-11
Carste
n
Kutzner
Small
f
i
x
for g_tu
n
e
_p
m
e
commit
|
commitdiff
|
tree
2012-05-23
C
a
rsten Kutzner
Revised g_
t
u
n
e_pme
commit
|
commitdiff
|
tree
2012-03-09
C
a
rs
t
en Kutz
n
er
M
erge "Improved wa
r
n
i
ng note wi
t
h
DD and periodic molecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten Kutzner
Ne
w
t
o
ol that
ex
t
racts dye dynamics fro
m
trajectories
commit
|
commitdiff
|
tree
2011-12-20
Car
s
ten Kutz
n
er
Added -d
h
dl to tpr file list, fixe
s
#855
commit
|
commitdiff
|
tree
2011-12-19
C
arsten Kutzner
Enforc
e
d rot
a
tio
n
commit
|
commitdiff
|
tree
2011-11-22
C
a
r
s
ten Kutzn
e
r
A
ctually -cpi an
d
-bcpo must not be identical
commit
|
commitdiff
|
tree
2011-10-31
Cars
t
en Kutzner
F
ix
e
d bug
#830 (segv in do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Cars
t
en
Kutzner
Rem
o
ve segv in
x
pm2p
s
, fixes #611
commit
|
commitdiff
|
tree
2011-08-26
Carsten Kutzne
r
Remove s
e
gv in xpm2p
s
, fixes #611
commit
|
commitdiff
|
tree
2011-08-25
Carsten
K
u
t
zner
Instead of
a
s
egv, m
d
r
un now gives an error msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten Kutzn
e
r
T
y
po
.
commit
|
commitdiff
|
tree
2011-07-29
C
ars
t
en Kutzner
Fixed calculati
o
n of max and mi
n
number of PM
E
-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutzne
r
Removed old-
f
as
h
ioned
M
P
E
logging cod
e
commit
|
commitdiff
|
tree
2011-07-11
Carsten Kutzner
Added t
w
o missing head
e
r
s
commit
|
commitdiff
|
tree
2011-07-06
Ca
r
sten
Kutzner
Added globsig
.
h to include/type
s
/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Kutzn
e
r
Flooding as harm
.
restr
a
int:
A
bort wh
e
n origin position
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Ku
t
zner
Checks for
zero-mass atoms in E
D
, better ordering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
C
a
rst
e
n Kutzne
r
Fix
e
d wrong e
r
ror message when using fl
o
oding cod
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Car
s
ten K
u
tzner
Fixed
bug #714:
deprec
a
ted structure in gettime
o
fday
commit
|
commitdiff
|
tree
2011-02-25
Carsten Ku
t
zner
Corre
c
ted output of a w
a
rning messag
e
.
commit
|
commitdiff
|
tree
2011-02-25
Carsten Kutzner
Added
the -fix opti
o
n t
o
g_tune_pme for tuning
o
f
rcoulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
C
a
rs
t
en Kutzner
Enforced
rot
a
tion
:
fix compiler wa
r
n
ing
commit
|
commitdiff
|
tree
2011-02-16
C
arsten Kutz
n
er
Merge branch 'release-4-5
-
patch
e
s'
commit
|
commitdiff
|
tree
2011-02-16
Carsten Kutz
n
er
Merge branc
h
'rele
a
se-4-5
-
p
a
tches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
Ca
r
sten Kutzner
Fixed int overfl
o
w happening
in genion when number
.
.
.
commit
|
commitdiff
|
tree
2011-01-13
Cars
t
e
n
Kutzner
Enforced rotation: added fit type
'poten
t
i
a
l
'
commit
|
commitdiff
|
tree
2011-01-04
Carsten Kutzn
e
r
Merg
e
b
ra
n
ch 're
l
ease-4-5-patches'
commit
|
commitdiff
|
tree
2010-12-02
Cars
t
e
n Kutz
n
er
Merge branc
h
'rele
a
se-4-5-patche
s
'
commit
|
commitdiff
|
tree
2010-11-30
Carsten Kut
z
ner
Merg
e
b
r
anch '
m
aster' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-11-26
Carsten
Kut
z
ner
E
n
forced
rotat
i
on: f
i
xed torque calculati
o
n for FLEX
.
.
.
commit
|
commitdiff
|
tree
2010-11-23
Carste
n
Kutzner
Merge branch
'
master' of g
i
t
.
g
romacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-11-23
Carste
n
Kutzn
e
r
E
n
fo
r
c
ed rot
a
tio
n
: cod
e
c
l
eanup
commit
|
commitdiff
|
tree
2010-11-18
Carsten Ku
t
zner
B
etter descr
i
p
tion of rotation options
commit
|
commitdiff
|
tree
2010-11-17
Carste
n
Kutzne
r
Removed unnecessary inc
l
ud
e
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kut
z
ner
Me
r
g
e b
r
anch
'
rotation'
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kutzner
Merge branch 're
l
ease
-
4-5-patches'
commit
|
commitdiff
|
tree
2010-11-15
Carst
e
n
Ku
t
zner
Merge bran
c
h
'rotation-4-5' into rotat
i
on
commit
|
commitdiff
|
tree
2010-11-15
Cars
t
en Kutz
n
e
r
En
f
orced rotation: define Gauss
i
a
n
n
orm
commit
|
commitdiff
|
tree
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