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Update TNG build system
2014-06-28
Magnus Lundbo
r
g
Upda
t
e TNG buil
d
sy
s
t
em
commit
|
commitdiff
|
tree
2014-06-28
Mark
A
braham
Use paral
l
el termi
n
o
logy more consistently
commit
|
commitdiff
|
tree
2014-06-28
n
g
oga
De
f
ault SD integrator
is n
o
w sd1 by
Nicu Gog
a
commit
|
commitdiff
|
tree
2014-06-27
Erik L
i
ndahl
Always se
t
b
-stat
e
po
s
res,
even if
identical t
o
a-state
commit
|
commitdiff
|
tree
2014-06-27
Er
i
k Li
n
d
ahl
Update g
_
density
t
o
h
andle bilayers better
commit
|
commitdiff
|
tree
2014-06-27
E
rik Lin
d
a
hl
Fix LJP
M
E Lorentz
-
Berthelot co
m
bination rules
commit
|
commitdiff
|
tree
2014-06-27
Rossen A
p
ostolov
C
ha
n
ged linking or
d
er to make E
x
t
r
ae work
.
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
indahl
Improve PDB I
/
O (keep
occupancy, b-facto
r
, element)
commit
|
commitdiff
|
tree
2014-06-27
Car
s
ten Kutzner
Remove obsolete pull-g
e
o
m
etry option 'positio
n
' fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland
S
chulz
F
i
x Phi Platf
o
rm
f
ile
f
or M
P
I
commit
|
commitdiff
|
tree
2014-06-27
Erik Linda
h
l
Avoid warnings abou
t
coupling when
fr
e
e_ener
g
y=no
commit
|
commitdiff
|
tree
2014-06-27
R
o
s
sen Apostolov
Added information about
dihedral rest
r
aints
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apos
t
olo
v
Remove instal
l
_ma
n
ifest
.
txt
d
uring make clea
n
.
commit
|
commitdiff
|
tree
2014-06-26
Mark Abraham
Merge "
M
er
g
e
r
elease-4-6 into release-5-0" into rele
a
se-5-0
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k
L
i
ndahl
Upda
t
ed
Amber GBSA pa
r
a
meters
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Ma
k
e source co
m
p
i
le
u
n
der Linux
X
32 ABI
commit
|
commitdiff
|
tree
2014-06-25
E
r
ik L
i
ndahl
Make
i
t harder for compiler to optimize aw
a
y SIMD CMake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Abraha
m
Manual fixes
commit
|
commitdiff
|
tree
2014-06-24
Magnus Lundb
o
rg
Impr
o
ved check to decide if to a
d
d
c
hain/
r
es
i
d
ue
.
commit
|
commitdiff
|
tree
2014-06-24
Dav
i
d van der Spo
e
l
Added ch
e
ck
i
n grom
p
p
f
o
r s
h
ells a
n
d inputrec issues
.
commit
|
commitdiff
|
tree
2014-06-24
Eri
k
Li
n
dahl
Fixed GROMOS assignment of
PRO-NH terminus to
r
sions
commit
|
commitdiff
|
tree
2014-06-24
E
r
ik Lindahl
Make sure duplicates bondeds are set from hac
k
b
l
ocks
commit
|
commitdiff
|
tree
2014-06-24
E
r
i
k Li
n
d
a
hl
C
l
ean up CMAP pl
a
cement in pa
r
ameter
list
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
A
d
ded mu
l
tisim
u
l
a
tion
i
nfo to lo
g
/output
commit
|
commitdiff
|
tree
2014-06-24
Rossen Apostolov
Extend version check
i
n
g
/w
a
rnings f
o
r checkpoint
c
o
n
t
inuatio
n
commit
|
commitdiff
|
tree
2014-06-23
Ro
s
sen Apostolov
Added
tip5p to th
e
list of watermodels i
n
s
o
me FF
.
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik
L
indahl
E
n
able 4-let
t
er resname in PDB
o
utp
u
t
,
k
e
e
ps m
o
re pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Eri
k
L
i
nd
a
h
l
Detect
n
o
n
-fatal warnings
w
hen trying C
F
lags for source
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
E
n
a
ble
x
vgr ou
t
p
u
t and
l
abels fo
r
g_prin
c
ip
a
l
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Disallow extracti
n
g
V
/F fr
o
m XT
C
files in g_
t
raj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Warn if using nsteps=
0
w
ithout conti
n
uation=yes
commit
|
commitdiff
|
tree
2014-06-21
Ve
d
ran Miletić
Use ${CMAKE_IN
S
T
A
L
L
_LIBDIR} as lib direc
t
ory for tng_io
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix g_mindist with pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Ros
s
en Apos
t
olov
Fixed typo in
o
plsaa ASPH
cha
r
g
e
s
.
commit
|
commitdiff
|
tree
2014-06-20
Rosse
n
Aposto
l
ov
Rem
o
ved u
n
used
p
aram
e
t
ers and cleanup of inputrec
.
commit
|
commitdiff
|
tree
2014-06-19
Roland S
c
hulz
Fi
x
ref
e
r
ror in constrai
n
t
pull
c
o
d
e
commit
|
commitdiff
|
tree
2014-06-19
Ro
s
sen Apostolov
Small typos in surface tension description
.
commit
|
commitdiff
|
tree
2014-06-19
Magnu
s
Lundborg
B
u
m
ped the TNG library to
t
he late
s
t v
e
rsion
.
commit
|
commitdiff
|
tree
2014-06-18
Erik Lindahl
Fixed CMake
2
.
8
.
12+ CUDA dylib bugs and wa
r
nings on
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
Rossen Apos
t
ol
o
v
Added referenc
e
to cmap in pdb2gmx
.
commit
|
commitdiff
|
tree
2014-06-18
Be
r
k Hess
F
ixed
s
ign error
i
n posres dvdl
commit
|
commitdiff
|
tree
2014-06-18
M
ar
k
Abraham
Made md
r
u
n
wa
r
n whe
n
generi
c
kernels are used
commit
|
commitdiff
|
tree
2014-06-17
Carlo
Ca
m
illoni
Fix a Replic
a
Exc
h
ange output proble
m
commit
|
commitdiff
|
tree
2014-06-17
Roland Schulz
Fix that ski
p
ping
fail
s
if t
a
rget is
2nd frame
commit
|
commitdiff
|
tree
2014-06-17
Berk Hess
Removed rou
n
d
ing issu
e
in nbnxn
E
w
a
ld tabl
e
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
Fixed
P
ME bug with
#
OpenMP-th
r
ead
s
a
l
arge prim
e
commit
|
commitdiff
|
tree
2014-06-14
Rossen Ap
o
st
o
lov
Adde
d
tip5pe water mod
e
l to opls
a
.
commit
|
commitdiff
|
tree
2014-06-14
Er
i
k L
i
ndahl
Ma
k
e sure figur
e
leg
e
nds are adapte
d
to
xmgr/xmgra
c
e
commit
|
commitdiff
|
tree
2014-06-13
B
erk Hess
Cha
n
g
e
d
a
p
pe
n
ding file name error message
commit
|
commitdiff
|
tree
2014-06-13
David van der Spoel
Fi
x
memo
r
y-usage error in g_chi
commit
|
commitdiff
|
tree
2014-06-13
R
o
la
n
d Schulz
Make nbnxn
t
emplat
e
and gener
a
ted
f
iles match
commit
|
commitdiff
|
tree
2014-06-13
Erik Lin
d
a
hl
Force g_bond to use
s
t
r
uctu
r
e file
commit
|
commitdiff
|
tree
2014-06-12
Erik L
i
n
dahl
Added dummy
mass for char
m
m TYR aroma
t
ic
v
s
ites
commit
|
commitdiff
|
tree
2014-06-12
B
e
rk Hess
Fixed perturbed wall interactions
commit
|
commitdiff
|
tree
2014-06-11
Berk
H
ess
D
ecoupled
r
epl_ex_nst from nstcalcenergy
commit
|
commitdiff
|
tree
2014-06-11
Ross
e
n Apostolov
Map
p
e
d
HI
S
1 to HSD
i
n c
h
a
rmm27
.
commit
|
commitdiff
|
tree
2014-06-11
Erik Lind
a
hl
Avoid
writ
i
ng xvgr
formatt
i
ng wit
h
-xvg none
commit
|
commitdiff
|
tree
2014-06-10
Erik Lind
a
hl
Process negati
v
e sigma
c
orrectly
wi
t
h combrule 2
o
r
3
commit
|
commitdiff
|
tree
2014-06-09
Ros
s
en Ap
o
stolov
Issue a warning for
u
sin
g
gmx_rms -prev
with large
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rossen
A
postolov
Install
libraries in
correc
t
dire
c
tories on
multiarch
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
Set
m
ake_ndx m
a
x name
l
ength and count to
1
02
4
commit
|
commitdiff
|
tree
2014-06-09
E
rik
Lin
d
ahl
Fixed the out
p
ut
f
ormat of g_prin
c
ipa
l
commit
|
commitdiff
|
tree
2014-06-09
Rossen A
p
os
t
olov
Fixed typo in d
e
s
cri
p
tion of
c
onversion factors
.
commit
|
commitdiff
|
tree
2014-06-09
E
rik Li
n
dahl
M
o
dify sing
l
e/double
EPS
t
o agree with ISO C
commit
|
commitdiff
|
tree
2014-06-07
Erik Linda
h
l
Adde
d
package
versi
o
n
to tng_io CMakelis
t
s
.
txt
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
Fix cons
t
raint virial with multiple time stepping
commit
|
commitdiff
|
tree
2014-06-05
M
ark Abr
a
ham
New q
u
otes
commit
|
commitdiff
|
tree
2014-06-04
Rossen Apostol
o
v
Update
d
C-/N-te
r
m
i
nal partial charges in
Amber03
.
f
f
.
commit
|
commitdiff
|
tree
2014-06-03
M
a
rk
A
brah
a
m
Use
RNG c
o
rrectly
for v-resc
a
le t
h
e
r
mostat
commit
|
commitdiff
|
tree
2014-06-01
Sz
i
lárd Páll
Add
q
uote on the k
T
-kj/mol conv
e
rsion factor
commit
|
commitdiff
|
tree
2014-06-01
E
r
ik Lindah
l
Fixed
t
ypo
i
n
manua
l
commit
|
commitdiff
|
tree
2014-05-31
David van der Spoel
Permit trjconv to read and write
velocities
w
it
h
T
NG
.
.
.
commit
|
commitdiff
|
tree
2014-05-30
M
a
rk Abrah
a
m
Fi
n
alize c
h
ange from
GMX_CPU_A
C
CELERATIO
N
to GMX_SIMD
commit
|
commitdiff
|
tree
2014-05-24
Rossen Ap
o
stolov
Sim
p
li
f
ied sec
t
ion "Porting"
.
commit
|
commitdiff
|
tree
2014-05-22
Ross
e
n Apostolov
Normal mode
s
don't work curr
e
ntly with virtua
l
sit
e
s
.
.
.
commit
|
commitdiff
|
tree
2014-05-22
Teemu Murtola
Fix stat
i
c grou
p
li
s
t
i
n
d
ic
e
s in s
e
lecti
o
n
prom
p
t
commit
|
commitdiff
|
tree
2014-05-22
Be
r
k Hes
s
Avoid ene
r
gy dr
i
ft wit
h
verlet-
b
uffer
-
tol
e
rance
commit
|
commitdiff
|
tree
2014-05-22
Mark Abraham
Add
f
atal errors for VV and twin-range MTS
commit
|
commitdiff
|
tree
2014-05-22
M
ark
Abraham
C
larifi
e
d
docs for us
e
of mdrun -nstlist
commit
|
commitdiff
|
tree
2014-05-20
J
u
stin L
e
mkul
Impro
v
ements to th
e
g_lie help d
e
scription
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen
A
p
os
t
olov
Adde
d
a note
about using di
r
ec
t
i
o
n-periodic pu
l
ling
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen Apostolov
Added a note
a
bout
u
nsuppo
r
ted Ver
l
et cutoff
+ Buckingham
.
commit
|
commitdiff
|
tree
2014-05-20
Mark Abr
a
ham
A
dd
n
o
te
a
b
o
ut correct cal
l
ing of wallcycle count
e
r
commit
|
commitdiff
|
tree
2014-05-18
M
a
rk
A
b
r
aham
Fix in
d
enting of
.
tpr parameter
dum
p
in mdrun log
file
commit
|
commitdiff
|
tree
2014-05-09
Alexe
y
S
hvet
s
ov
F
ix
cla
n
g 3
.
5
warnings
reg
a
rdi
n
g
*abs*
commit
|
commitdiff
|
tree
2014-05-09
Berk Hess
Minor tweaks t
o
the DD set
u
p
commit
|
commitdiff
|
tree
2014-05-09
R
o
l
a
nd Schulz
F
i
x
co
m
parison of array to N
U
LL
commit
|
commitdiff
|
tree
2014-05-09
Roland
Schulz
Merge "Merge
bra
n
ch release-4-6 into release-
5
-0" into
.
.
.
commit
|
commitdiff
|
tree
2014-05-09
Rola
n
d Schulz
Fi
x
Ope
n
MP scope erro
r
commit
|
commitdiff
|
tree
2014-04-29
B
erk Hess
Re
m
oved tru
n
cation of nrd
f
in v-rescale thermostat
commit
|
commitdiff
|
tree
2014-04-24
Magnus Lundborg
More efficient TNG selection group creation
commit
|
commitdiff
|
tree
2014-04-23
Berk Hess
Fixed nbnxn FE l
i
s
t
allocation issue
commit
|
commitdiff
|
tree
2014-04-21
Mic
h
a
el Shirts
Issue warnings for pot
e
n
t
i
a
l switch
w/o defining sw
i
t
ch
.
.
.
commit
|
commitdiff
|
tree
2014-04-16
Magnu
s
Lundborg
Fixed bug inver
t
ing c
o
mpression precis
i
on
.
commit
|
commitdiff
|
tree
2014-04-16
Mark Abra
h
am
Fix an
d
si
m
plify ver
s
ion
ma
t
ching for running tests
commit
|
commitdiff
|
tree
2014-04-07
M
ark Ab
r
aham
Fix i
n
v
a
l
id dereference in g_tune_pm
e
commit
|
commitdiff
|
tree
2014-04-07
Erik
L
indahl
Ma
k
e sure wa
t
e
r
optimization is
d
isabled for esoteric
.
.
.
commit
|
commitdiff
|
tree
2014-04-07
T
e
emu
Murtola
Dox
y
g
en docume
n
tatio
n
for version
.
h
commit
|
commitdiff
|
tree
2014-04-03
Mark Abr
a
h
a
m
Move string-parsing co
d
e to where it c
a
n be reused
commit
|
commitdiff
|
tree
2014-04-02
Roland S
c
hulz
A
dd
d
o
c
for spec
.
va
l
ues o
f
GMX_MAXBAC
K
UP
commit
|
commitdiff
|
tree
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