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Fixed essential dynamics (ED) continuation from .cpt for reference=average
2013-12-23
Carst
e
n Kut
z
n
er
Fix
e
d e
s
sential dynamics (ED) continuation
fr
o
m
.
cp
t
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Carsten
K
utz
n
er
Prop
e
rly finalize MPI on mdr
u
n
-
ve
r
si
o
n
.
F
i
xes #1313
commit
|
commitdiff
|
tree
2013-06-26
Carsten
Kutz
n
er
Fix
e
d -npstring command line
argument i
n
g_tune
_
p
m
e
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
Fi
x
ed ca
l
culation
o
f
s
lab buffer
si
z
e for flex
i
ble
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Cars
t
en K
u
tz
n
er
Fix for a
r
are co
n
d
itio
n
in fl
e
xible rotation poten
t
ial
s
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten Kutzn
e
r
Code cleanup in enforced rotation modu
l
e
, remove warni
n
gs
.
commit
|
commitdiff
|
tree
2013-05-16
Carst
e
n K
u
t
zn
e
r
Choose
t
he PBC image of each
rotat
i
o
n g
r
oup a
t
om depending
commit
|
commitdiff
|
tree
2013-04-29
Carsten Kutzner
E
valuate enforced ro
t
ation
po
t
eni
a
l with Ve
r
let, fixes
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten K
u
tzner
Essential dynamics: fixed legend in ED
.
xvg output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
Carsten Kutzn
e
r
Made g_tune_pme work
w
ith
4
.
6 if
u
ser sets "-p" co
m
mand
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
C
a
rsten Ku
t
zner
Fixed th
e
MPI recogni
t
ion string i
n
g
_tune_pm
e
commit
|
commitdiff
|
tree
2013-01-22
C
a
r
ste
n
K
u
tzner
Mov
e
d a few com
m
ents back
into p
o
si
t
ion
commit
|
commitdiff
|
tree
2013-01-17
Carsten Kutzner
Add
e
d note about make_e
d
i a
n
d
flooding in ED paragraph
commit
|
commitdiff
|
tree
2013-01-16
Carsten
Kutzner
Made g_t
u
ne
_
pme work correctly again with
t
hread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Carsten Ku
t
zne
r
Essential d
y
na
m
i
c
s
outp
u
t
file n
o
w in
.
xvg
f
orm
a
t
commit
|
commitdiff
|
tree
2012-12-20
Carsten Ku
t
zn
e
r
Small fix for g_tu
n
e_pme
commit
|
commitdiff
|
tree
2012-12-20
Car
s
ten Kutzner
Essential
dynamics: fixed restarts when ED g
r
oup has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kutzn
e
r
M
ad
e
g_tune_pme work
correctly
w
h
en ir
-
>init
_
s
tep > 0
commit
|
commitdiff
|
tree
2012-10-16
Carsten Kutzner
Made g_tune_pme read (ns/day) from 4
.
6 md
.
l
o
g output
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carste
n
Kutzner
Rem
o
ved obsolete hint in error message
.
commit
|
commitdiff
|
tree
2012-08-07
Carsten
K
u
t
zner
Fixe
d
essential dynamics / flo
o
di
n
g group PBC serial
commit
|
commitdiff
|
tree
2012-08-06
Ca
r
sten Kutzn
e
r
Fixed
calculation of pr
o
ject
i
on
f
or
STAR an
d
/
o
r SORI
commit
|
commitdiff
|
tree
2012-08-06
Carsten
K
u
tzn
e
r
Add
e
d comm
e
nt in get
_
stru
c
ture about w
h
ic
h
st
r
u
ctur
e
s
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Ca
r
ste
n
Kutzner
Fixed se
g
v in essential dyn
a
mi
c
s module
commit
|
commitdiff
|
tree
2012-07-06
Carst
e
n Kutzner
Enfo
r
ced rotati
o
n: PBC/re
s
tar
t
fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Kutzner
Small fix for g_tu
n
e_pme
commit
|
commitdiff
|
tree
2012-05-23
Cars
t
en Kutzner
Revised g_tune_p
m
e
commit
|
commitdiff
|
tree
2012-03-09
Carste
n
Kut
z
ner
Merge "Impro
v
ed warning note with
D
D and periodic
molecules
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Car
s
ten Ku
t
zner
New t
o
ol that extrac
t
s dye dyn
a
mi
c
s from t
r
ajectories
commit
|
commitdiff
|
tree
2011-12-20
Carsten Kutzner
A
d
d
ed -dhdl to t
p
r
fil
e
lis
t
,
fixes
#
8
5
5
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kutzner
E
n
fo
r
ced rotation
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutz
n
er
A
c
tually -cpi
a
nd -bcpo must not be identica
l
commit
|
commitdiff
|
tree
2011-10-31
Carsten
K
utzner
Fixe
d
bug #830 (seg
v
i
n do_dssp)
commit
|
commitdiff
|
tree
2011-08-31
Ca
r
s
t
e
n Kutzner
Remo
v
e segv in xpm2ps, fixes #611
commit
|
commitdiff
|
tree
2011-08-25
C
a
rst
e
n Ku
t
zner
In
s
t
ead
o
f
a
segv
,
mdrun now gives
an error msg
if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Car
s
ten Kutzner
Typo
.
commit
|
commitdiff
|
tree
2011-07-29
Carste
n
Ku
t
zner
Fixed
c
alculation of ma
x
a
n
d min number
o
f PM
E
-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
C
ar
s
ten Kutzner
Ad
d
ed two missing head
e
r
s
commit
|
commitdiff
|
tree
2011-07-06
Carste
n
Kutzner
Added globsig
.
h to include/
t
yp
e
s/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten
K
utzne
r
Flooding as h
a
rm
.
r
estraint: Abort when ori
g
in po
s
iti
o
n
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Car
s
ten Kutzner
Check
s
for z
e
ro-mass atoms
in ED, better ordering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carsten
K
ut
z
ner
Fixed wrong error message
when using flooding c
o
d
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
C
arsten Kutzner
Fixed bug #714: depr
e
cated str
u
cture in gettime
o
f
d
a
y
commit
|
commitdiff
|
tree
2011-02-25
Carst
e
n Kutzner
Corrected output o
f
a war
n
ing message
.
commit
|
commitdiff
|
tree
2011-02-25
Carst
e
n K
u
tzner
A
d
ded the -fix option to g_tune_pme
for tun
i
ng of rcoulo
m
b
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
Carsten Ku
t
z
ner
Merge b
r
an
c
h 'releas
e
-4-5-pa
t
ch
e
s' of gi
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-02-16
C
a
rsten
K
utzner
Fixe
d
int o
v
erflow happening in genion when
n
umber
.
.
.
commit
|
commitdiff
|
tree
2011-01-04
ckutzne
Fixed i
n
c
o
n
ven
i
ent output
f
ile nam
e
s if -
s
ep is use
d
.
.
.
commit
|
commitdiff
|
tree
2010-12-02
ckut
z
ne
F
i
xed typo
.
commit
|
commitdiff
|
tree
2010-10-29
Carsten Kutzn
e
r
F
i
xed
s
egv
i
n
g
mx_hbon
d
commit
|
commitdiff
|
tree
2010-10-22
C
arsten
K
utz
n
e
r
Fix
e
d s
e
gv in
g
_
p
o
t
e
n
t
ial
.
Field output has
now also
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
Carsten Ku
t
zne
r
Fixed segv in make_edi
when no ref
e
rence
s
tructure
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
Carsten Kutz
n
er
Fixe
d
segv in make_edi when n
o
reference structure
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Carsten Kutzner
Resubmi
t
ted changes tha
t
w
e
re accidentally undone by
.
.
.
commit
|
commitdiff
|
tree
2010-01-13
Ca
r
sten Kutzner
M
er
g
e b
r
a
nch 'mas
t
er
'
of git@git
.
gr
o
macs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-01-13
Carste
n
Kutzner
Moved ro
u
tines that collect group coo
r
ds
for co
m
parison
.
.
.
commit
|
commitdiff
|
tree
2009-12-21
Carsten Kutzner
Merge bran
c
h
'
master' of git@
g
it
.
gromacs
.
o
rg:
g
roma
c
s
commit
|
commitdiff
|
tree
2009-12-21
Carsten
K
utzner
Essential dynamics: fixed segfault
when using sd2 i
n
te
g
rato
r
commit
|
commitdiff
|
tree
2009-12-21
Carsten Ku
t
zner
Es
s
ent
i
a
l
d
y
nami
c
s:
f
i
xed segf
a
ult when u
s
ing s
d
2 integr
a
t
o
r
commit
|
commitdiff
|
tree
2009-11-30
Carsten Kut
z
ner
g_tune_pme now does pro
p
er cleanup also with pu
l
l
s
i
m
ulation
s
commit
|
commitdiff
|
tree
2009-10-21
Carst
e
n Kut
z
ner
g
_
tune
_
pme now also accepts < 3 no
d
es, al
s
o
outputs
.
.
.
commit
|
commitdiff
|
tree
2009-10-12
Carsten Kutzner
Merge branch '
m
aster' of git@g
i
t
.
g
romacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-10-12
Carsten
Kutzn
e
r
cycle counters can now be
reset by a (hidden) mdrun
.
.
.
commit
|
commitdiff
|
tree
2009-09-16
Carsten Kutzne
r
Me
r
g
e
branch 'master' of git@git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-09-16
Carste
n
Kut
z
n
e
r
Fixed
format conversions i
n
gmx_tune_pme
.
c
commit
|
commitdiff
|
tree
2009-09-07
Ca
r
s
ten Kutzn
e
r
Edsam: Added t
h
e
possibility
t
o
flood towards a ce
r
tai
n
.
.
.
commit
|
commitdiff
|
tree
2009-08-11
Cars
t
en Kutzner
Fixe
d
u
nin
i
tializ
e
d var
i
able in gmx_tune_pme
.
c
commit
|
commitdiff
|
tree
2009-07-30
Car
s
ten Ku
t
zner
Merge branch '
m
aster' of g
i
t@git
.
gromacs
.
or
g
:groma
c
s
commit
|
commitdiff
|
tree
2009-07-29
Carst
e
n Kutzner
Merge b
r
anch 'master' of git@git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2009-07-28
C
a
r
st
e
n Kutzner
set in
i
t_
s
tep
on pme o
n
ly nodes
when
counter rese
t
ting
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Carsten Kutz
n
er
Co
u
nte
r
res
e
t
ting also on the PME only nodes
commit
|
commitdiff
|
tree
2009-07-16
C
arste
n
Kutzner
Check md
.
log to ensure GMX_RESE
T
_COUNTERS was p
a
ssed
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Carsten Kutzner
Check
whe
t
her mpirun accepts -x
o
p
t
i
o
n
commit
|
commitdiff
|
tree
2009-07-15
Carst
e
n
Kutzner
M
e
rge branc
h
'm
a
ster' of git
@
g
i
t
.
gromacs
.
org
:
gr
o
mac
s
commit
|
commitdiff
|
tree
2009-07-15
Ca
r
sten Kut
z
ner
Se
v
eral imp
r
ove
m
ents to g
m
x_t
u
n
e
_pme
commit
|
commitdiff
|
tree
2009-07-07
Ca
r
ste
n
Kutzner
M
e
r
ge branch '
m
aster'
of git@git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2009-07-07
Carst
e
n Kutzner
Removed u
n
used m
_
rvec*
f
unctio
n
s in ve
c
.
h (unneeded
.
.
.
commit
|
commitdiff
|
tree
2009-07-07
Carsten Kutzner
Made the optional GMX_BARRIE
R
S
work with se
p
arate PME
.
.
.
commit
|
commitdiff
|
tree
2009-07-06
Carsten Ku
t
zne
r
O
utput the co
r
re
c
t numbe
r
of files in read
_
tpr_pul
l
xf_files
commit
|
commitdiff
|
tree
2009-06-23
Carsten Kutzner
F
ixed chec
k
_oo memory corrupti
o
n problem
commit
|
commitdiff
|
tree
2009-06-22
C
a
rsten Kutzner
Me
r
ge branch 'master' of gi
t
@
g
i
t
.
gromacs
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2009-06-19
Carsten Kutzner
Re
m
oved
all static va
r
iables in
e
dsam
.
c
commit
|
commitdiff
|
tree