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Update TNG build system
2014-06-28
Magn
u
s L
u
n
dborg
U
pdate TNG bu
i
ld system
commit
|
commitdiff
|
tree
2014-06-28
Mark Abraham
U
s
e p
a
rallel terminology more consistentl
y
commit
|
commitdiff
|
tree
2014-06-28
ngo
g
a
Default
SD inte
g
r
a
t
o
r is
n
ow sd1 by
Nicu Goga
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Always set b-
s
t
a
te p
o
sr
e
s, even if identical to a
-
s
t
a
te
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Update g_density to han
d
le bilayers better
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Fi
x
L
JPME Lorentz-Berth
e
lot
c
om
b
inatio
n
rules
commit
|
commitdiff
|
tree
2014-06-27
Ro
s
sen
Apostolov
Chan
g
ed lin
k
ing order to make Extrae w
o
rk
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Lin
d
ahl
Improve PDB I
/
O (keep occu
p
an
c
y
,
b-fa
c
tor, element
)
commit
|
commitdiff
|
tree
2014-06-27
Carsten Kutzner
Remove
obsolete pull
-
g
e
o
metry optio
n
'position' fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland
Schu
l
z
Fix Phi Platform file
f
or
MPI
commit
|
commitdiff
|
tree
2014-06-27
Eri
k
Linda
h
l
Avoid w
a
rn
i
ngs abo
u
t c
o
upling
w
hen free_energ
y
=no
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apos
t
olov
Added in
f
ormation about
d
ihedral restraint
s
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostol
o
v
Rem
o
ve install_manifest
.
txt during make clean
.
commit
|
commitdiff
|
tree
2014-06-26
Mark A
b
raham
Merge "Mer
g
e re
l
ease-
4
-6 in
t
o rel
e
ase-5-0" into
rel
e
a
s
e-5-0
commit
|
commitdiff
|
tree
2014-06-25
Erik Li
n
dahl
Updated A
m
ber GBSA param
e
ter
s
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k Lindahl
Make source comp
i
le un
d
er Linux X32
ABI
commit
|
commitdiff
|
tree
2014-06-25
E
r
ik Lindahl
M
ake it h
a
rder
for co
m
pil
e
r to
o
pti
m
ize awa
y
SIMD
CMake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Abraham
Ma
n
ual fixes
commit
|
commitdiff
|
tree
2014-06-24
M
agnus L
u
ndborg
Impro
v
ed
c
heck to deci
d
e if
t
o add chain/residue
.
commit
|
commitdiff
|
tree
2014-06-24
Da
v
id
van der
S
poel
Added check i
n
grompp
f
or sh
e
lls and in
p
utrec is
s
ue
s
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fixed
GRO
M
OS assignment of PRO-NH te
r
mi
n
u
s torsions
commit
|
commitdiff
|
tree
2014-06-24
Erik Lind
a
hl
M
a
ke
sure du
p
l
icates
b
ondeds are s
e
t from hackblock
s
commit
|
commitdiff
|
tree
2014-06-24
Er
i
k
L
indahl
Clean
up CMAP placem
e
nt in parameter list
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Adde
d
multisimulati
o
n info to lo
g
/
o
u
tput
commit
|
commitdiff
|
tree
2014-06-24
Rossen Apost
o
lov
Extend
v
er
s
ion checki
n
g
/
warning
s
for
c
hec
k
point continuat
i
on
commit
|
commitdiff
|
tree
2014-06-23
Rossen Aposto
l
o
v
Ad
d
e
d
t
i
p5p to t
h
e list of water
m
odels
in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
En
a
ble
4
-letter resname in PDB
o
utpu
t
, keeps m
o
re pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Dete
c
t
n
on-fatal
w
arnings when trying
CFlag
s
for source
commit
|
commitdiff
|
tree
2014-06-23
Erik
Li
n
d
ahl
Enable xvgr output and label
s
f
o
r
g_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik
Lindahl
Disal
l
ow extracting
V/F from
XTC files
i
n g_tra
j
commit
|
commitdiff
|
tree
2014-06-23
Eri
k
Lindahl
W
a
rn if using
n
steps=0 w
i
t
h
o
u
t conti
n
u
a
t
ion=
y
es
commit
|
commitdiff
|
tree
2014-06-21
Vedran Miletić
Use ${CMAKE_IN
S
T
ALL_LIBDIR} as li
b
dir
e
c
t
o
ry fo
r
tng_io
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Be
r
k He
s
s
Fi
x
g_min
d
i
s
t wi
t
h pbc
=
XY
commit
|
commitdiff
|
tree
2014-06-20
Rosse
n
Apostolov
F
ixe
d
typo in o
p
lsaa ASPH char
g
es
.
commit
|
commitdiff
|
tree
2014-06-20
Rossen Apostolov
Removed unu
s
ed param
e
ters and clean
u
p
o
f inputrec
.
commit
|
commitdiff
|
tree
2014-06-19
Roland Schulz
Fix ref err
o
r in c
o
n
straint p
u
l
l
c
o
de
commit
|
commitdiff
|
tree
2014-06-19
Rossen Ap
o
st
o
lo
v
Small typos
in surface tension description
.
commit
|
commitdiff
|
tree
2014-06-19
Mag
n
us Lundb
o
rg
B
u
mped
t
h
e TNG library to th
e
latest version
.
commit
|
commitdiff
|
tree
2014-06-18
E
r
i
k
Lindahl
Fixed CMake 2
.
8
.
12+ CUDA dylib bugs an
d
warnin
g
s on
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
Ros
s
en A
p
ostol
o
v
Added reference to cmap in pdb2gmx
.
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
Fix
e
d sig
n
error
in posr
e
s dvdl
commit
|
commitdiff
|
tree
2014-06-18
Mark Abraham
M
a
de mdrun warn when generic ke
r
ne
l
s a
r
e
u
s
e
d
commit
|
commitdiff
|
tree
2014-06-17
C
a
rlo
Camilloni
Fix a R
e
plica Exchang
e
output problem
commit
|
commitdiff
|
tree
2014-06-17
R
o
land
Schulz
Fi
x
th
a
t skipp
i
ng fails
i
f t
a
rget is 2nd fram
e
commit
|
commitdiff
|
tree
2014-06-17
Be
r
k Hess
Rem
o
ved r
o
unding
i
ssu
e
in nbnxn Ewal
d
table
commit
|
commitdiff
|
tree
2014-06-14
B
e
r
k Hess
Fixed PME bug with #
O
penMP-th
r
eads
a large prime
commit
|
commitdiff
|
tree
2014-06-14
Rossen Aposto
l
ov
Added tip5pe wat
e
r mode
l
to oplsa
.
commit
|
commitdiff
|
tree
2014-06-14
Erik Linda
h
l
Make sure fi
g
ure legends ar
e
adapted to xmgr/xmgrace
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Changed appen
d
ing f
i
le name error message
commit
|
commitdiff
|
tree
2014-06-13
Dav
i
d
va
n
der Spoel
Fix memory-usage error in g_chi
commit
|
commitdiff
|
tree
2014-06-13
Roland S
c
hulz
Make
n
bnxn template and gene
r
ated files matc
h
commit
|
commitdiff
|
tree
2014-06-13
E
rik Linda
h
l
Force g_bond to use s
t
ructure file
commit
|
commitdiff
|
tree
2014-06-12
E
rik L
i
ndahl
Added dummy mass for charmm TYR a
r
o
m
atic vsit
e
s
commit
|
commitdiff
|
tree
2014-06-12
Berk
H
ess
Fix
e
d perturbed wall
inter
a
ctions
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Dec
o
u
pled
r
epl_e
x
_nst from ns
t
calcenergy
commit
|
commitdiff
|
tree
2014-06-11
Rossen
A
postolov
Map
p
ed HI
S
1 to HSD i
n
ch
a
rmm27
.
commit
|
commitdiff
|
tree
2014-06-11
Erik Lindahl
Avoid
w
riting
x
vgr form
a
tting wit
h
-
xv
g
none
commit
|
commitdiff
|
tree
2014-06-10
Er
i
k Lindahl
P
r
ocess ne
g
a
t
ive sigma
correctly with combrule 2 o
r
3
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
Issue
a
warning for usi
n
g gmx_rms -
p
rev wit
h
l
arge
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
I
n
stall lib
r
aries
in
cor
r
ect directories on multiar
c
h
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
S
e
t make
_
ndx max name length and count to
1024
commit
|
commitdiff
|
tree
2014-06-09
Eri
k
Lindahl
Fixed the output format of g_principal
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
Fixed
typo
i
n description o
f
c
onversion factors
.
commit
|
commitdiff
|
tree
2014-06-09
Erik Lindahl
Modify single/double EPS
t
o
agree
w
ith IS
O
C
commit
|
commitdiff
|
tree
2014-06-07
E
r
i
k
L
i
n
dahl
Added
package versio
n
to tng_io CMakelists
.
txt
commit
|
commitdiff
|
tree
2014-06-05
Be
r
k Hess
Fix constrai
n
t virial with mul
t
i
ple
t
ime stepping
commit
|
commitdiff
|
tree
2014-06-05
Ma
r
k Ab
r
aham
New
quotes
commit
|
commitdiff
|
tree
2014-06-04
Rossen
Apostol
o
v
Updated C-/N-
t
e
r
minal partial
c
harges in Amber03
.
ff
.
commit
|
commitdiff
|
tree
2014-06-03
M
a
r
k Abraham
Us
e
RNG cor
r
ectly for v-rescale t
h
ermo
s
ta
t
commit
|
commitdiff
|
tree
2014-06-01
Szil
á
rd Páll
Add quo
t
e
on the kT-kj
/
m
ol
c
onver
s
ion factor
commit
|
commitdiff
|
tree
2014-06-01
Er
i
k
L
indahl
Fixed
t
ypo in m
a
nual
commit
|
commitdiff
|
tree
2014-05-31
Da
v
id v
a
n
d
er Spoel
Per
m
it trj
c
onv to
read
and
w
r
ite vel
o
ci
t
ie
s
with TN
G
.
.
.
commit
|
commitdiff
|
tree
2014-05-30
Mark Abraham
Fi
n
a
l
ize change fr
o
m GMX_CP
U
_ACCELERAT
I
ON to GMX_S
I
MD
commit
|
commitdiff
|
tree
2014-05-24
R
o
ssen Apo
s
tolov
Simplifi
e
d section
"
P
orting"
.
commit
|
commitdiff
|
tree
2014-05-22
Rossen Apostolov
Normal m
o
d
e
s do
n
't work
c
ur
r
e
n
tly with vi
r
tual
s
i
t
es
.
.
.
commit
|
commitdiff
|
tree
2014-05-22
Teemu Murtola
Fix stati
c
gro
u
p lis
t
i
n
d
ices i
n
selecti
o
n pr
o
mpt
commit
|
commitdiff
|
tree
2014-05-22
B
erk Hess
Avo
i
d ener
g
y
d
r
i
ft
w
ith verle
t
-buffer
-
tolerance
commit
|
commitdiff
|
tree
2014-05-22
Mark Abraham
Add fata
l
errors f
o
r VV a
n
d
twin-
r
a
n
ge MTS
commit
|
commitdiff
|
tree
2014-05-22
Mark Abraham
Cla
r
ified
docs
f
or use of mdrun -nstlist
commit
|
commitdiff
|
tree
2014-05-20
Justin Lemkul
Imp
r
ovements to the g_lie
help description
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen Apostolov
Added a note about
u
si
n
g directi
o
n
-
peri
o
dic
p
ul
l
ing
.
commit
|
commitdiff
|
tree
2014-05-20
Ro
s
sen Aposto
l
o
v
Added a note
a
bou
t
un
s
u
pported
V
erlet cutoff + Bucki
n
gham
.
commit
|
commitdiff
|
tree
2014-05-20
Mark Abraham
Add
not
e
about correct cal
l
ing o
f
wallcycle counter
commit
|
commitdiff
|
tree
2014-05-18
Mar
k
Abraham
Fix indenting of
.
tpr parameter dump in
m
drun log file
commit
|
commitdiff
|
tree
2014-05-09
Alexey
Shve
t
s
ov
Fix clang
3
.
5
warnings regar
d
i
ng
*
a
b
s*
commit
|
commitdiff
|
tree
2014-05-09
Berk Hess
Mino
r
t
weaks to the DD setup
commit
|
commitdiff
|
tree
2014-05-09
R
oland Sc
h
ulz
Fix co
m
p
a
rison of ar
r
ay to NULL
commit
|
commitdiff
|
tree
2014-05-09
Roland Schulz
Merge
"
M
e
rge
branch release-4-6
into release-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-05-09
Rolan
d
Schulz
Fix Ope
n
MP s
c
ope error
commit
|
commitdiff
|
tree
2014-04-29
Ber
k
Hess
R
emoved tr
u
ncat
i
o
n
o
f nrdf in v-rescale thermostat
commit
|
commitdiff
|
tree
2014-04-24
Mag
n
us Lundborg
More e
f
ficient TNG select
i
on
group creation
commit
|
commitdiff
|
tree
2014-04-23
Be
r
k He
s
s
Fixed
nbnxn FE li
s
t allocat
i
o
n
iss
u
e
commit
|
commitdiff
|
tree
2014-04-21
Michael
Shirts
Issue warnings for
p
ot
e
ntial
switch w/o defining switch
.
.
.
commit
|
commitdiff
|
tree
2014-04-16
Magnus Lun
d
borg
Fix
e
d bug inverting
c
ompre
s
sion precision
.
commit
|
commitdiff
|
tree
2014-04-16
Mark
A
b
raham
Fix an
d
s
implify v
e
rs
i
on ma
t
ching for
r
un
n
ing te
s
ts
commit
|
commitdiff
|
tree
2014-04-07
Mark Abraham
Fix
i
nvalid derefe
r
ence in g_tune_pme
commit
|
commitdiff
|
tree
2014-04-07
E
rik Lin
d
ahl
Make sure wat
e
r
o
p
t
im
i
zati
o
n
is disa
b
l
e
d for esot
e
ric
.
.
.
commit
|
commitdiff
|
tree
2014-04-07
T
e
emu
Mu
r
tola
D
oxygen documentati
o
n fo
r
ve
r
si
o
n
.
h
commit
|
commitdiff
|
tree
2014-04-03
M
a
rk Abraham
Move
s
tring
-
parsing code to whe
r
e it can be reuse
d
commit
|
commitdiff
|
tree
2014-04-02
Rolan
d
Schul
z
Add d
o
c
for spe
c
.
va
l
ues
o
f GM
X
_MAXBACKUP
commit
|
commitdiff
|
tree
next