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Fix reference to vmdio.c to be vmdio.cpp
2016-04-14
Carsten Kutzner
Cor
r
e
c
ted value of electric conv
e
rsion factor
f
in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
Clean
-
up co
d
e for
swa
p
coords
.
commit
|
commitdiff
|
tree
2016-03-18
Car
s
ten Kutzner
C
lar
i
f
ied li
c
e
n
se t
e
xt in th
e
.
tex manual
commit
|
commitdiff
|
tree
2016-03-17
C
a
rs
t
en
Kut
z
n
e
r
F
i
x membed
initializat
i
on
commit
|
commitdiff
|
tree
2016-02-18
Carsten Kutzner
Sma
l
l update
to
re
f
erenc
e
manual
commit
|
commitdiff
|
tree
2016-02-16
Ca
r
s
t
en Kutz
n
er
C
h
anged no
r
m(
.
.
.
) > 0 co
n
dit
i
on to norm2
(
.
.
.
)
>
0
i
n
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Improved/enlarg
e
d Fig
.
4
.
9 i
n
m
a
nual
for better readability
commit
|
commitdiff
|
tree
2016-01-20
C
a
rs
t
en Kutzn
e
r
Made g_
t
u
n
e_pme
work
w
ith -cpi
-
deffnm combination
commit
|
commitdiff
|
tree
2015-11-17
Carst
e
n
K
utzne
r
Fixed -n
p
str
i
ng
c
ommand line argument
i
n gmx tune_pme
commit
|
commitdiff
|
tree
2015-11-13
C
arsten Kutzner
Ion/w
a
t
e
r
position swappin
g
for multip
l
e ion
t
y
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carste
n
Kutz
n
e
r
Described the
c
ompu
t
ational electroph
y
siology
.
m
d
p
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
C
ars
t
en Ku
t
zner
Extr
a
o
p
tio
n
s f
o
r computational ele
c
trophysiology
.
commit
|
commitdiff
|
tree
2015-10-07
Carsten Kutzner
Code c
l
ea
n
up in swapc
o
o
r
ds
.
cp
p
commit
|
commitdiff
|
tree
2015-10-02
Cars
t
e
n
Kutzner
Fi
x
ed a bug
i
n
computat
i
on
a
l
electrophys
i
ology with DD
commit
|
commitdiff
|
tree
2015-07-15
Carsten Kutz
n
er
Removed
information
a
bout obs
o
lete
.
edo
f
i
le form
a
t
commit
|
commitdiff
|
tree
2014-12-09
Ca
r
sten Kutzne
r
Ma
k
e tune_pme understa
n
d the "-n
s
teps"
o
pti
o
n
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten Kutzner
F
ixed a typo in the manual
.
commit
|
commitdiff
|
tree
2014-11-12
C
a
rsten
K
u
t
zner
Updated some
.
mdp file variables to use "-" instead
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Ca
r
sten Kutzner
Fix or
d
er of ED/s
w
a
p blocks
d
uring
c
heckpoi
n
t
reading
.
commit
|
commitdiff
|
tree
2014-10-01
Ca
r
s
ten Ku
t
zner
Allow
g
mx tune_pme to skip the check
for command-li
n
e
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
C
arsten K
u
tzner
Fixed output of
e
igen
v
alues in g_
c
ovar
.
F
i
xes #1575
commit
|
commitdiff
|
tree
2014-06-27
Car
s
ten Kut
z
ner
Remove
obsolete pull-geometry op
t
ion 'position' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Cars
t
e
n Ku
t
z
ner
R
e
-
use gmx_w
i
thin
_
t
ol f
r
om math
/
utilities instead of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carsten
Kutz
n
er
Fix documentatio
n
of
s
wap/en
u
ms
.
h
commit
|
commitdiff
|
tree
2014-03-28
C
a
rsten K
u
tzner
Fix d
o
cumentation
i
ssues f
o
r interactive MD modu
l
e
.
commit
|
commitdiff
|
tree
2014-03-26
Carsten Kutzner
D
o
cume
n
tat
i
on house-kee
p
ing in fil
e
sw
a
p
coords
.
c
commit
|
commitdiff
|
tree
2014-03-14
C
arsten Kutzner
Avoi
d
c
r
o
s
s pr
o
duc
t
with zero vector in rota
t
ional
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Ca
r
s
ten
Kutzner
The van der Waals radius
m
ust e
q
ual the Coul
o
m
b
r
adius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Carsten Kutzner
S
mall e
n
hancemen
t
of
com
p
utational e
l
e
ctrophysiolo
g
y
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
C
a
rsten Kut
z
ner
Allo
w
for "computationa
l
el
e
c
trophysiology" simulati
o
ns
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
Carste
n
K
u
tzner
Move pull
co
d
e to
sep
a
r
ate
s
u
b
d
ire
c
tory
commit
|
commitdiff
|
tree
2014-01-11
Carsten Kutzner
Move essent
i
al dynamics
/
flooding code to s
e
parate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
Ca
r
ste
n
Kutzner
Read essen
t
ial dynamic
s
data from c
h
eckpoint a
t
correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Carsten Kutzner
Re
m
oved a few typos in three G
e
r
m
an quotes
.
commit
|
commitdiff
|
tree
2013-12-26
Carsten Kutzne
r
Pass on de
f
ault value
o
f radstep in
m
ake_edi
commit
|
commitdiff
|
tree
2013-12-25
Cars
t
en Kutzner
Essenti
a
l dynamics: move
bNee
d
DoEdsam evaluation to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
C
a
r
sten Kutzner
Fixed essential dy
n
amic
s
(ED) cont
i
n
u
ation fro
m
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Ca
r
sten K
u
tzner
Properly finalize MPI on
md
r
un -versi
o
n
.
F
ixes #1313
commit
|
commitdiff
|
tree
2013-06-26
C
a
rsten K
u
t
zne
r
Fi
x
ed -npstring
comman
d
l
i
ne argumen
t
i
n
g_tune_p
m
e
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
Fixed calculat
i
on of slab buffer size for flexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Ca
r
sten Kutzn
e
r
Fix for
a
r
are
condition i
n
f
l
exi
b
le rota
t
i
on potent
i
als
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten Kutzner
C
o
d
e
cleanu
p
in
enforced
r
ot
a
tion
m
odule, remove warnings
.
commit
|
commitdiff
|
tree
2013-05-16
C
a
rsten
K
utz
n
er
Choos
e
the
P
BC image of each r
o
tation group atom dependin
g
commit
|
commitdiff
|
tree
2013-04-29
Carsten K
u
tzne
r
E
v
a
l
uate enforced rot
a
tio
n
p
otenial wit
h
Verlet, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten Kutzner
Es
s
ential dynamics: fixed legend
i
n ED
.
x
v
g outpu
t
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten K
u
tzner
M
ade g_tune_pme wo
r
k with 4
.
6 if
u
ser sets "-p" command
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Carsten Kutzner
Fi
x
ed the MPI reco
g
ni
t
i
o
n s
t
ring
i
n
g_t
u
n
e_pme
commit
|
commitdiff
|
tree
2013-01-22
Carsten Kutzner
M
ove
d
a few comments
back into p
o
sition
commit
|
commitdiff
|
tree
2013-01-17
Carsten Kutzner
Add
e
d no
t
e
about mak
e
_edi and flooding in ED parag
r
aph
commit
|
commitdiff
|
tree
2013-01-16
Carsten
K
utzn
e
r
Made g_t
u
ne_pm
e
w
o
rk correctly
again wi
t
h
threa
d
-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
C
a
r
sten Kutzner
Essenti
a
l
d
ynamics ou
t
put file
n
ow
in
.
xvg
format
commit
|
commitdiff
|
tree
2012-12-20
Cars
t
en Kutzner
S
m
all fix
for
g_tun
e
_pme
commit
|
commitdiff
|
tree
2012-12-20
Carste
n
Kutzner
E
s
sen
t
i
a
l dy
n
ami
c
s
:
fix
e
d restarts
w
hen ED
g
r
oup h
a
s
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carst
e
n K
u
tzner
M
a
de g_tune_p
m
e wor
k
correctly when ir->init_step
>
0
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
Made g_tune_pme read (
n
s/day) from 4
.
6 md
.
l
og outpu
t
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
Remove
d
obsolet
e
h
int in error message
.
commit
|
commitdiff
|
tree
2012-08-07
Carst
e
n
Kutzn
e
r
Fixed
essen
t
ial dynami
c
s
/
flooding
g
roup P
B
C serial
commit
|
commitdiff
|
tree
2012-08-06
Car
s
ten Ku
t
z
n
er
F
i
x
ed calcula
t
ion of pro
j
ection f
o
r STAR and/or SORI
commit
|
commitdiff
|
tree
2012-08-06
Carsten Kutzn
e
r
Added comment in
g
et_s
t
ruc
t
ure ab
o
ut which structures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
Fixed segv in e
s
sential dynamics module
commit
|
commitdiff
|
tree
2012-07-06
Carste
n
Kutzner
Enf
o
rced rotatio
n
: P
B
C/r
e
start fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Kutzner
Small fix for g_tune_pme
commit
|
commitdiff
|
tree
2012-05-23
Cars
t
en Ku
t
zne
r
Revi
s
ed g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten
K
u
tzner
Merge
"
Im
p
ro
v
ed war
n
ing not
e
with DD and periodic molecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten
K
utzner
New
t
ool tha
t
e
xtracts d
y
e d
y
namics from traject
o
ries
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutzne
r
A
dded -dhdl to tpr file list, fixes #85
5
commit
|
commitdiff
|
tree
2011-12-19
C
a
rsten
Kutzner
Enforced rotat
i
on
commit
|
commitdiff
|
tree
2011-11-22
Carsten
Kutzner
Act
u
al
l
y
-
cpi and -bcpo mu
s
t
n
o
t be identical
commit
|
commitdiff
|
tree
2011-10-31
Carsten Kut
z
ner
Fix
e
d bug #830 (segv in do
_
dssp)
commit
|
commitdiff
|
tree
2011-08-31
Ca
r
sten K
u
tzner
Re
m
ov
e
s
e
g
v in xpm2p
s
, fixes
#
6
1
1
commit
|
commitdiff
|
tree
2011-08-26
Carsten
K
utzner
Remove segv in xpm2ps
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-25
C
a
rsten
Kutz
n
er
Instead of
a
s
e
gv
,
mdrun now gives an error msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Carsten
K
u
tz
n
er
T
y
po
.
commit
|
commitdiff
|
tree
2011-07-29
Carste
n
Kutzner
Fixed c
a
lcu
l
ation of
m
ax
and min number of PME-
o
nly
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Carsten Ku
t
z
n
er
Remov
e
d
old-f
a
shion
e
d
M
P
E
logging c
o
d
e
commit
|
commitdiff
|
tree
2011-07-11
Carsten
Kutzn
e
r
Added two m
i
ssi
n
g header
s
commit
|
commitdiff
|
tree
2011-07-06
Carsten
K
ut
z
ner
Added globsi
g
.
h to include/ty
p
es/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Car
s
ten Kutzner
F
l
ooding as ha
r
m
.
restrain
t
: Abort
w
hen origin posit
i
on
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Chec
k
s for zer
o
-
mass atoms in ED
,
better ordering
of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten Kutzn
e
r
Fixed wr
o
n
g
erro
r
mess
a
ge when
u
sing f
l
ooding c
o
d
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
C
arsten
K
u
t
z
ner
Fixed bug #714: de
p
r
e
c
a
ted stru
c
ture in gettimeofday
commit
|
commitdiff
|
tree
2011-02-25
Carsten Kutzner
Corrected output of a warning
m
e
ssage
.
commit
|
commitdiff
|
tree
2011-02-25
Carsten K
u
t
zner
Added the -f
i
x
o
p
t
i
on
to
g
_t
u
ne
_
pme fo
r
t
uning o
f
rcoulomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
Ca
r
ste
n
Kutzner
Enforced rotation: fix
compiler warning
commit
|
commitdiff
|
tree
2011-02-16
C
a
rsten Kutzn
e
r
Me
r
ge branc
h
'
r
elease-4-5-patches'
commit
|
commitdiff
|
tree
2011-02-16
Carsten Kutzner
M
e
rge bran
c
h
'release-4
-
5-patches'
o
f git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
Carsten Kutzner
Fixed int overflow happening in
g
enion when number
.
.
.
commit
|
commitdiff
|
tree
2011-01-13
Car
s
t
en
Kutzner
En
f
orced rota
t
ion:
add
e
d fi
t
type 'pot
e
nt
i
al'
commit
|
commitdiff
|
tree
2011-01-04
Ca
r
sten Kutzner
Me
r
ge branch 'release-4
-
5
-pa
t
ches'
commit
|
commitdiff
|
tree
2010-12-02
Ca
r
sten Kutzne
r
Merge branch
'release-4-5
-
patches'
commit
|
commitdiff
|
tree
2010-11-30
Carsten K
u
tzner
Merge branc
h
'mas
t
er' of
git
.
gromac
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-11-26
Carsten Kutzner
Enforced rota
t
ion: fix
e
d torque calc
u
lation for FLEX
.
.
.
commit
|
commitdiff
|
tree
2010-11-23
Carsten Kutzner
Merge branch 'master
'
of git
.
gromacs
.
org
:
g
r
omacs
commit
|
commitdiff
|
tree
2010-11-23
Carsten Kutzne
r
En
f
o
r
ce
d
r
o
tation: code cle
a
nup
commit
|
commitdiff
|
tree
2010-11-18
Car
s
te
n
Kutzne
r
Better d
e
s
c
ription
o
f rotation
optio
n
s
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kutzner
Remove
d
unne
c
essa
r
y
i
nclude
commit
|
commitdiff
|
tree
2010-11-17
Carsten
Kutzn
e
r
Merge
b
r
anch 'rotation'
commit
|
commitdiff
|
tree
2010-11-17
Carsten Kutzner
Merge bra
n
ch 'release-4-5-pat
c
hes
'
commit
|
commitdiff
|
tree
2010-11-15
Carsten
Kutzner
Merge bran
c
h 'rot
a
tion-4-5' into
r
otation
commit
|
commitdiff
|
tree
2010-11-15
Carsten Kutzner
En
f
o
rced rota
t
ion: de
f
ine
G
aussian n
o
r
m
commit
|
commitdiff
|
tree
next