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Support 4 sized cluster for GPU NBL search
2018-01-08
Ca
r
s
t
en Kutzner
Fi
x
a fe
w
ty
p
os i
n
S
IMD documentati
o
n
commit
|
commitdiff
|
tree
2017-12-20
Carsten
K
u
t
zn
e
r
Destruct MDModules/forc
e
provider
s
prio
r
to c
a
lling
.
.
.
commit
|
commitdiff
|
tree
2017-12-19
Carsten K
u
tzner
F
ix electric field
.
mdp
documentation
commit
|
commitdiff
|
tree
2017-08-10
Carsten Ku
t
zner
Corrected the PDF manual to refl
e
ct
t
hat al
l
tools
.
.
.
commit
|
commitdiff
|
tree
2017-08-03
Carsten Kutz
n
er
Added missing
.
mdp
f
ile d
o
cumentation for the enforced
.
.
.
commit
|
commitdiff
|
tree
2017-07-10
Carsten Kutzner
Ad
d
ed missing
.
mdp f
i
le d
o
cumentation for th
e
e
nforced
.
.
.
commit
|
commitdiff
|
tree
2017-06-23
Carsten Kutzn
e
r
F
ixed #2206 IM
D
inte
r
face malfunctions
commit
|
commitdiff
|
tree
2017-06-16
Carsten Kutzner
Fixed a consi
s
t
e
ncy check in make_edi for
f
lood
i
ng
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutz
n
er
M
oved esse
n
t
i
al dynamics initia
l
i
zation call into do_md()
commit
|
commitdiff
|
tree
2017-06-09
Carsten Kutzner
Adopt and
document implementation p
o
l
icy for
M
D modules
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kutzner
Minor header f
i
le cleanup in
E
D, IMD and CompEL mo
d
ule
s
commit
|
commitdiff
|
tree
2017-04-19
Carsten Kutzner
Re
m
ove unused forward
d
eclaratio
n
s of t_commrec i
n
.
.
.
commit
|
commitdiff
|
tree
2017-03-02
Carsten Kutzne
r
Remove u
n
necess
a
ry include
commit
|
commitdiff
|
tree
2016-11-16
Carsten
K
u
tzn
e
r
I
n
creased the default reset st
e
p to 150
0
in gmx tune_pme
commit
|
commitdiff
|
tree
2016-11-15
Carsten K
u
tzner
Fixed typo
i
n
m
embed
.
cpp
commit
|
commitdiff
|
tree
2016-04-14
Cars
t
en Kutzner
Corr
e
ct
e
d
v
alue of electric c
o
nversion
f
actor f in
.
.
.
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzner
C
l
ea
n
-up co
d
e for s
w
a
p
coords
.
commit
|
commitdiff
|
tree
2016-03-18
Carsten Kutzner
Clarified l
i
cen
s
e
t
e
xt i
n
the
.
tex manual
commit
|
commitdiff
|
tree
2016-03-17
Carsten Kutzner
Fix
m
embed in
i
tialization
commit
|
commitdiff
|
tree
2016-02-18
Carsten
Kutzne
r
Small updat
e
to ref
e
rence manu
a
l
commit
|
commitdiff
|
tree
2016-02-16
Carsten Kutzner
Chang
e
d norm
(
.
.
.
)
>
0
cond
i
t
i
o
n
t
o
norm
2
(
.
.
.
) >
0 in
.
.
.
commit
|
commitdiff
|
tree
2016-02-16
Carsten Ku
t
z
ner
Im
p
roved/enl
a
r
ged Fig
.
4
.
9 in
m
anual for better
re
a
dability
commit
|
commitdiff
|
tree
2016-01-20
Carsten Kutzner
Ma
d
e g_tune_pme work
w
ith -cpi -
d
ef
f
n
m
combinatio
n
commit
|
commitdiff
|
tree
2015-11-17
Carsten Kutzner
Fixed -npstring command
li
n
e argu
m
e
nt in gmx tune_pme
commit
|
commitdiff
|
tree
2015-11-13
Carsten Kutzner
Ion/wa
t
e
r
p
o
sition swapping f
o
r
multipl
e
i
on types
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutz
n
er
D
escri
b
ed the computat
i
onal elect
r
ophysiology
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
C
a
rsten Kut
z
ner
Extra options for computati
o
na
l
electrophysi
o
log
y
.
commit
|
commitdiff
|
tree
2015-10-07
Cars
t
e
n Kutzner
C
ode cleanup in
s
w
a
pcoo
r
ds
.
cpp
commit
|
commitdiff
|
tree
2015-10-02
Carsten Kutzner
Fixed a bug
in
c
omputational electrophysiolog
y
with
D
D
commit
|
commitdiff
|
tree
2015-07-15
C
a
rsten Ku
t
zner
Removed i
n
f
o
rmation ab
o
ut obsolete
.
edo file format
commit
|
commitdiff
|
tree
2014-12-09
Carsten
K
u
tzner
Make tun
e
_pme un
d
e
rsta
n
d th
e
"-ns
t
e
ps" op
t
ion
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2014-12-08
Carsten
K
utzner
Fixed
a
t
y
p
o
in
the manual
.
commit
|
commitdiff
|
tree
2014-11-12
C
arsten
K
u
tzner
Updated
s
ome
.
mdp file variables to use
"-" ins
t
e
a
d
.
.
.
commit
|
commitdiff
|
tree
2014-10-20
Carste
n
Kutzne
r
Fix order of ED/swap blocks during chec
k
point
r
eading
.
commit
|
commitdiff
|
tree
2014-10-01
Carsten K
u
tzner
Allo
w
g
mx t
u
n
e
_pme
t
o skip th
e
check for command-line
.
.
.
commit
|
commitdiff
|
tree
2014-08-15
Car
s
ten Kutzner
Fixed output of eige
n
values i
n
g
_
covar
.
F
i
xes #1575
commit
|
commitdiff
|
tree
2014-06-27
Ca
r
sten Kutzn
e
r
R
e
move
o
bso
l
ete pull-geometry o
p
tio
n
'positi
o
n' from
.
.
.
commit
|
commitdiff
|
tree
2014-04-10
Carsten Kut
z
ner
Re-use gmx_wit
h
i
n
_t
o
l fro
m
m
a
t
h/utiliti
e
s inst
e
ad of
.
.
.
commit
|
commitdiff
|
tree
2014-03-31
Carsten Ku
t
zner
F
ix
d
oc
u
mentation of swap
/
enu
m
s
.
h
commit
|
commitdiff
|
tree
2014-03-28
Carst
e
n Kutzner
F
i
x docu
m
entation issues for interactive M
D
module
.
commit
|
commitdiff
|
tree
2014-03-26
C
arsten Kutzner
D
o
cumenta
t
i
on house-k
e
eping in file swapcoo
r
ds
.
c
commit
|
commitdiff
|
tree
2014-03-14
Carsten Ku
t
z
ner
Avoid
cross product with zero vector in ro
t
a
t
i
onal
.
.
.
commit
|
commitdiff
|
tree
2014-03-14
Carsten Kutz
n
er
The va
n
d
e
r Waals r
a
dius must equal the Coulomb
r
a
dius
.
.
.
commit
|
commitdiff
|
tree
2014-02-16
Cars
t
en Kut
z
ne
r
Sma
l
l enhancement of com
p
utational ele
c
trophy
s
iology
.
.
.
commit
|
commitdiff
|
tree
2014-01-28
C
a
r
s
ten Ku
t
zner
Allow for "computational
e
le
c
trop
h
ysiol
o
gy" s
i
mu
l
ations
.
.
.
commit
|
commitdiff
|
tree
2014-01-13
C
arsten Kutzner
Mov
e
pull code to s
e
p
a
ra
t
e subdire
c
tory
commit
|
commitdiff
|
tree
2014-01-11
Carsten Kutzne
r
M
ove es
s
ential d
y
nami
c
s
/ flooding code to separate
.
.
.
commit
|
commitdiff
|
tree
2014-01-10
C
a
rsten Kutzner
Read essential
d
ynamics data from checkpoint at correct
.
.
.
commit
|
commitdiff
|
tree
2014-01-05
Car
s
ten Kut
z
ner
Rem
o
ved a few
typos in thr
e
e German quotes
.
commit
|
commitdiff
|
tree
2013-12-26
C
arsten Kut
z
ner
P
a
ss o
n
default value of
radst
e
p in make_edi
commit
|
commitdiff
|
tree
2013-12-25
Carsten Kutzner
Essential
dy
n
amics: move
b
Ne
e
dDoEdsam
e
valuation t
o
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
Cars
t
en Kutzner
F
i
x
e
d ess
e
n
tial
d
ynami
c
s (ED) continua
t
ion
from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-08-01
Carsten Kutzne
r
Properly fina
l
ize MPI on mdrun
-
v
ersi
o
n
.
Fix
e
s #1313
commit
|
commitdiff
|
tree
2013-06-26
Carsten K
u
tzner
Fixed
-npstring command line
argument in g_tune_pme
commit
|
commitdiff
|
tree
2013-05-28
Carste
n
Kutzner
Fixed calculati
o
n
of
s
lab
b
uff
e
r size for
flexi
b
le
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
Fix for
a
rare
condition
i
n flexible r
o
tat
i
on po
t
e
n
tials
.
commit
|
commitdiff
|
tree
2013-05-27
Carsten
K
u
tz
n
er
Code cleanup in enforced rotation m
o
dule
,
remove wa
r
nings
.
commit
|
commitdiff
|
tree
2013-05-16
Cars
t
en Kutzner
Choose the
P
B
C imag
e
of ea
c
h
rotati
o
n
group a
t
o
m depending
commit
|
commitdiff
|
tree
2013-04-29
C
arst
e
n
Kutzner
Evaluate enforced
r
otati
o
n potenial wit
h
Verlet, fi
x
es
.
.
.
commit
|
commitdiff
|
tree
2013-03-08
Carsten K
u
tzner
E
s
s
ential dyna
m
i
c
s
:
fixed legend in ED
.
xvg output
.
.
.
commit
|
commitdiff
|
tree
2013-02-18
C
a
r
s
t
e
n
Ku
t
z
ner
M
a
de
g
_tu
n
e_
p
me work
with 4
.
6
if u
s
er sets "-p" comm
a
nd
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
Ca
r
sten Kutz
n
er
Fix
e
d the MP
I
r
e
cognition
s
tring in g_tune_pme
commit
|
commitdiff
|
tree
2013-01-22
Carsten K
u
tzner
Moved a
f
ew comments back i
n
to po
s
i
t
i
o
n
commit
|
commitdiff
|
tree
2013-01-17
Carsten K
u
t
zn
e
r
Added note about
m
ake_edi and flooding in ED paragraph
commit
|
commitdiff
|
tree
2013-01-16
Carsten Kutz
n
er
M
ade
g_tune_p
m
e work
c
orrec
t
l
y
a
gain
w
ith
thread
-
MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-14
Ca
r
sten Kutzner
Essential
dynamics o
u
tput file now in
.
xvg form
a
t
commit
|
commitdiff
|
tree
2012-12-20
Carsten
Kutzner
Small fix for g
_
t
u
n
e_pme
commit
|
commitdiff
|
tree
2012-12-20
Car
s
t
en
K
utzne
r
E
sse
n
t
i
a
l
d
y
namics: fixed restarts whe
n
ED gr
o
u
p
has
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Carsten Kut
z
ne
r
Made g_
t
une_pme wor
k
correctly
w
hen ir->init_step >
0
commit
|
commitdiff
|
tree
2012-10-16
Car
s
te
n
Kutzner
Made g_tune_p
m
e read (ns/day
)
from 4
.
6 md
.
log
outpu
t
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Carste
n
K
utzner
Re
m
oved obsolete
hin
t
in error message
.
commit
|
commitdiff
|
tree
2012-08-07
Car
s
t
e
n Kutzner
Fixe
d
esse
n
t
i
a
l
dynamics
/ f
l
ooding group PBC serial
commit
|
commitdiff
|
tree
2012-08-06
Cars
t
en
Kutzner
Fi
x
ed cal
c
ulatio
n
o
f
projection for STAR and/or SORI
commit
|
commitdiff
|
tree
2012-08-06
C
a
r
sten Kutzner
A
d
d
e
d comment
i
n g
e
t
_st
r
ucture abou
t
which structures
.
.
.
commit
|
commitdiff
|
tree
2012-08-03
Carsten Kutzner
Fi
x
ed segv i
n
essenti
a
l dynamics mod
u
l
e
commit
|
commitdiff
|
tree
2012-07-06
Carsten Kut
z
ner
E
nforced ro
t
ation: PBC
/
restart fix
commit
|
commitdiff
|
tree
2012-06-11
Carsten Ku
t
zner
Small fix fo
r
g_tu
n
e_pme
commit
|
commitdiff
|
tree
2012-05-23
Carsten Kut
z
ner
R
e
vised g_tune_pme
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kutzner
Merge "Improved warnin
g
note w
i
th D
D
and periodic mole
c
ule
s
.
.
.
commit
|
commitdiff
|
tree
2012-01-23
Carsten Kutzner
N
e
w tool that extracts
dye d
y
namics from t
r
aje
c
t
o
ries
commit
|
commitdiff
|
tree
2011-12-20
Carsten
K
utzner
Added -dhdl
t
o tpr file list, fixes #
8
55
commit
|
commitdiff
|
tree
2011-12-19
Carsten Kutzner
Enforced
rotation
commit
|
commitdiff
|
tree
2011-11-22
Carsten Kutzner
Actually -
c
pi and -bcpo
m
ust no
t
be ident
i
cal
commit
|
commitdiff
|
tree
2011-10-31
C
arsten Ku
t
zner
Fixed bug #830 (segv in do_
d
ssp)
commit
|
commitdiff
|
tree
2011-08-31
Car
s
ten Kutzner
Remove se
g
v in x
p
m
2
p
s
,
f
ixe
s
#611
commit
|
commitdiff
|
tree
2011-08-26
C
ar
s
ten Kutzner
Remov
e
segv in xpm2ps
,
fixes #611
commit
|
commitdiff
|
tree
2011-08-25
C
arsten Kutzner
Instead of
a
segv, mdrun n
o
w gives an er
r
or msg if
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Car
s
ten Kutzner
Typo
.
commit
|
commitdiff
|
tree
2011-07-29
Carsten
K
u
t
zner
F
ixed calcula
t
ion o
f
max and min
n
umber of PME-only
.
.
.
commit
|
commitdiff
|
tree
2011-07-11
Cars
t
en Kutzner
Removed old-fashioned MPE logging code
commit
|
commitdiff
|
tree
2011-07-11
Ca
r
s
te
n
Ku
t
zner
Added two missing header
s
commit
|
commitdiff
|
tree
2011-07-06
Carsten Kutzner
Added gl
o
bs
i
g
.
h
to
include/types/Makefile
.
am
commit
|
commitdiff
|
tree
2011-05-30
Carsten Kut
z
n
e
r
F
looding as harm
.
restrai
n
t
:
Abort when origin posit
i
on
.
.
.
commit
|
commitdiff
|
tree
2011-03-30
Carsten Kutzner
Checks for zero-mass
a
t
oms in ED, better o
r
d
ering of
.
.
.
commit
|
commitdiff
|
tree
2011-03-03
Carst
e
n
Kut
z
n
er
F
ixed
w
rong error message
when us
i
ng flooding cod
e
.
.
.
commit
|
commitdiff
|
tree
2011-03-01
Carsten Kutzner
F
i
xed bug #71
4
: d
e
preca
t
ed structure in gett
i
meofday
commit
|
commitdiff
|
tree
2011-02-25
Carste
n
Kutzner
Corr
e
c
te
d
output of a warning message
.
commit
|
commitdiff
|
tree
2011-02-25
Carst
e
n Kutzne
r
Added the -fix o
p
tion to
g
_tune_pme fo
r
tuning of rco
u
lomb
.
.
.
commit
|
commitdiff
|
tree
2011-02-17
C
a
rsten Kutzner
Enforc
e
d r
o
t
a
tion:
f
ix com
p
iler warning
commit
|
commitdiff
|
tree
2011-02-16
Carsten
Kutzne
r
Merge
b
ranch '
r
e
l
ea
s
e
-4-5-pa
t
ches'
commit
|
commitdiff
|
tree
next