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Make selections ignore \r in input
2014-07-08
Teemu Murtola
Make
selec
t
io
n
s
i
gnore \r
in i
n
p
ut
commit
|
commitdiff
|
tree
2014-07-07
Mar
k
Abraham
Fix
tarball and install, particularly for I
N
ST
A
LL
commit
|
commitdiff
|
tree
2014-07-05
Mag
n
us Lundborg
F
i
x bug causing reading next fram
e
n
o
t to
s
top
.
commit
|
commitdiff
|
tree
2014-07-05
M
a
g
n
u
s Lu
n
dbor
g
Fix tng_num_frame_set
s
_get() with no frame sets
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu Mu
r
t
o
la
Reinstantiate unsorted index group che
c
k
commit
|
commitdiff
|
tree
2014-07-05
R
oland Sc
h
ulz
A
d
d running
tes
t
s to install-guide
commit
|
commitdiff
|
tree
2014-07-05
Teemu
Murtola
Update so
m
e ins
t
all
a
tion-relat
e
d docs
commit
|
commitdiff
|
tree
2014-07-01
Mark
A
braham
F
i
x
GMock
t
o
work on MSVC
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Refe
r
to
"mixed"
p
recision in user-fa
c
ing
documen
t
ation
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
es
s
T
ak
e
LJ-PME i
n
to accou
n
t for table spacing
commit
|
commitdiff
|
tree
2014-06-29
E
r
ik
L
i
ndahl
F
i
x
ed free energy with
L
J-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
C
o
nvert
install
g
uide to ma
r
kdown
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Merge "Merge releas
e
-4-6
i
nto release-5-0"
into release-5-0
commit
|
commitdiff
|
tree
2014-06-29
B
erk Hess
Upda
t
ed
LJ-PME documentation
commit
|
commitdiff
|
tree
2014-06-29
R
o
sse
n
Apos
t
olov
Use cosistent style when referri
n
g
to fo
r
c
e fields
.
commit
|
commitdiff
|
tree
2014-06-29
Teemu
M
u
rtola
R
emove some hardcoded
selection
string buffe
r
s
commit
|
commitdiff
|
tree
2014-06-29
Roland Schul
z
Fix detection of i386
i
n
tmpi
commit
|
commitdiff
|
tree
2014-06-29
Erik Li
n
dahl
Ena
b
le rtp angle/dihedral entries not connected
by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Micha
e
l
S
hirts
Allow p
r
inting potential energies to dhdl
.
x
v
g
f
ile
commit
|
commitdiff
|
tree
2014-06-29
David van der Spoel
Fi
x
e
s #1532, SEGV in g_current
.
commit
|
commitdiff
|
tree
2014-06-29
Roland
S
c
hu
l
z
Me
r
ge
"Merge branch 'rel
e
ase-4-6' i
n
to release-5
-
0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Rola
n
d Schul
z
Fix error
for no 64bit
f
il
e
supp
o
rt
commit
|
commitdiff
|
tree
2014-06-28
Erik
L
i
ndahl
Fixed
CMAP
g
eneration for alan
i
ne dipe
p
tide s
p
ecial
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
M
a
gnus Lundbor
g
Upd
a
t
e
T
N
G build sy
s
tem
commit
|
commitdiff
|
tree
2014-06-28
Mark Abraham
Use par
a
l
l
el
t
ermi
n
ology mo
r
e consistentl
y
commit
|
commitdiff
|
tree
2014-06-28
ngoga
Defau
l
t SD integr
a
to
r
is now sd1 by
N
icu Gog
a
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Alway
s
set b
-
state posres, even if identical to a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
in
d
a
hl
Update
g
_den
s
it
y
to handle b
i
layers
b
etter
commit
|
commitdiff
|
tree
2014-06-27
Er
i
k
Lindahl
Fix L
J
PME Lor
e
ntz-Berthelot combination rules
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostolo
v
C
h
a
nged
li
n
king order to ma
k
e E
x
trae
w
ork
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Improve PDB I/O (keep oc
c
u
p
ancy,
b
-
fac
t
or, element)
commit
|
commitdiff
|
tree
2014-06-27
Carsten Kutzne
r
R
emove
o
bs
o
l
e
t
e pull-geometry option 'position' from
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland
S
chulz
Fi
x
Phi Platfor
m
file
f
o
r MPI
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
A
void
w
arni
n
gs
a
bo
u
t coupl
i
ng
w
hen free_e
n
ergy=no
commit
|
commitdiff
|
tree
2014-06-27
Ross
e
n Ap
o
stolov
Added informa
t
ion about dih
e
d
r
al re
s
traints
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Aposto
l
ov
Remov
e
install_manifest
.
txt
d
uring m
a
ke clean
.
commit
|
commitdiff
|
tree
2014-06-26
Mark
A
braham
Mer
g
e "Mer
g
e release-4-
6
i
nto release-5-0" into release-5-0
commit
|
commitdiff
|
tree
2014-06-25
Erik Lin
d
a
hl
Up
d
ated
Am
b
er GB
S
A paramet
e
rs
commit
|
commitdiff
|
tree
2014-06-25
Erik Li
n
dahl
Make
s
o
u
rce compile under Linu
x
X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k
L
indahl
M
ake
i
t
hard
e
r fo
r
compiler to
optimize away S
I
MD CMak
e
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark A
b
raham
Manual fix
e
s
commit
|
commitdiff
|
tree
2014-06-24
Magnus Lundborg
Improved check
to deci
d
e if to add chain/residue
.
commit
|
commitdiff
|
tree
2014-06-24
Davi
d
van der Spoel
Add
e
d che
c
k in grompp f
o
r s
h
ells and inputrec
i
s
s
u
es
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lind
a
hl
Fixed GROM
O
S assignment of PRO
-
N
H
te
r
m
i
n
us
t
orsio
n
s
commit
|
commitdiff
|
tree
2014-06-24
E
r
ik Lind
a
hl
Make sure duplicates bonded
s
are set from
h
a
c
kblocks
commit
|
commitdiff
|
tree
2014-06-24
Erik
L
i
ndahl
Clean up CMAP placem
e
nt in parame
t
er list
commit
|
commitdiff
|
tree
2014-06-24
E
r
ik Linda
h
l
A
dded multi
s
imulation info to
l
o
g
/o
u
tput
commit
|
commitdiff
|
tree
2014-06-24
Rossen
Apostolov
Extend ve
r
sion che
c
king/w
a
r
n
ings fo
r
checkp
o
int c
o
nt
i
nuation
commit
|
commitdiff
|
tree
2014-06-23
Rossen
Apo
s
to
l
ov
A
d
ded tip
5
p to the list of watermodels in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
Er
i
k Lin
d
ahl
Enab
l
e 4-letter re
s
nam
e
in PDB output,
keeps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Linda
h
l
Detect n
o
n-fatal wa
r
nings whe
n
trying CFlags for source
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Enable xv
g
r
output and labels for g_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik Lin
d
ahl
Disallo
w
extrac
t
ing V
/
F from XTC files in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
War
n
if using nsteps=0
w
it
h
out continuati
o
n=yes
commit
|
commitdiff
|
tree
2014-06-21
Ved
r
an
Miletić
Use ${CM
A
KE_INSTAL
L
_
L
IBDIR} as l
i
b di
r
e
c
tory for tng_io
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix g_min
d
i
st with
pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Ross
e
n Ap
o
stolov
Fixed
t
ypo in
opl
s
a
a
AS
P
H charge
s
.
commit
|
commitdiff
|
tree
2014-06-20
Ros
s
en Apostolov
Re
m
oved unused
param
e
ters and
clea
n
up of inpu
t
rec
.
commit
|
commitdiff
|
tree
2014-06-19
Rola
n
d Schu
l
z
Fix
r
ef e
r
ro
r
in constraint pu
l
l
code
commit
|
commitdiff
|
tree
2014-06-19
R
o
ssen Apostolov
Small typos in surface tension description
.
commit
|
commitdiff
|
tree
2014-06-19
Magnus Lundbor
g
Bumpe
d
the
T
NG library to the latest v
e
rsion
.
commit
|
commitdiff
|
tree
2014-06-18
Erik Lindahl
Fixed CMa
k
e 2
.
8
.
12+ C
U
DA dylib bu
g
s and
w
arnings o
n
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
R
o
ssen Apostolov
Added r
e
ference to cmap in pdb2gmx
.
commit
|
commitdiff
|
tree
2014-06-18
B
erk Hess
Fixe
d
sign error i
n
posre
s
dvdl
commit
|
commitdiff
|
tree
2014-06-18
Mark
A
braham
Made mdrun
w
a
r
n
when generic
kernels
a
re used
commit
|
commitdiff
|
tree
2014-06-17
Ca
r
lo Camill
o
ni
F
i
x
a Replica
E
xchange output
p
roblem
commit
|
commitdiff
|
tree
2014-06-17
Roland Schulz
Fix that skipping fails if ta
r
g
e
t
is
2
nd fram
e
commit
|
commitdiff
|
tree
2014-06-17
Berk H
e
ss
R
emoved ro
u
n
d
ing issue in
nbn
x
n Ewald t
a
b
l
e
commit
|
commitdiff
|
tree
2014-06-14
B
e
r
k Hess
Fixed PME bu
g
with #Op
e
nMP-
t
hre
a
ds a l
a
rge prime
commit
|
commitdiff
|
tree
2014-06-14
Rossen
Apostolov
Ad
d
e
d
t
i
p5pe water model
t
o
oplsa
.
commit
|
commitdiff
|
tree
2014-06-14
Erik
L
in
d
a
h
l
Mak
e
sure figure legen
d
s are adapted to xmgr
/
xmg
r
ace
commit
|
commitdiff
|
tree
2014-06-13
Ber
k
Hess
Changed appendi
n
g
f
ile
name error me
s
sage
commit
|
commitdiff
|
tree
2014-06-13
David van der Sp
o
el
Fix memory-usage
error i
n
g_
c
hi
commit
|
commitdiff
|
tree
2014-06-13
Roland Schulz
M
ake
n
bnx
n
template a
n
d ge
n
e
r
ated files
m
atch
commit
|
commitdiff
|
tree
2014-06-13
Erik L
i
ndahl
Force g_b
o
nd to us
e
struc
t
ure fi
l
e
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindah
l
Added
dummy mass for char
m
m TYR aromatic vsi
t
es
commit
|
commitdiff
|
tree
2014-06-12
B
erk Hess
Fi
x
e
d perturbed wall interactions
commit
|
commitdiff
|
tree
2014-06-11
Be
r
k Hess
Decouple
d
repl_ex_
n
st from
ns
t
calcen
e
rgy
commit
|
commitdiff
|
tree
2014-06-11
Rossen Apostolov
Mapped HIS1 to HSD in char
m
m27
.
commit
|
commitdiff
|
tree
2014-06-11
Erik Li
n
dahl
Avoid writ
i
ng xvgr
f
o
rmatting with
-
xvg
none
commit
|
commitdiff
|
tree
2014-06-10
Erik Lindahl
Process negat
i
v
e
s
i
g
ma cor
r
e
ctly
w
ith c
o
mbrul
e
2 or 3
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
Issue a warnin
g
f
or
using gmx_rms -pr
e
v with large
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
I
nstall libraries in corr
e
c
t
d
ire
c
t
o
ries on multiarch
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
Set mak
e
_ndx
m
ax
name lengt
h
and
c
ount t
o
1
024
commit
|
commitdiff
|
tree
2014-06-09
E
r
ik L
i
ndahl
Fixed the outp
u
t format of g_pr
i
n
cipal
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostolov
F
i
xed typo i
n
de
s
cript
i
on o
f
conversion factors
.
commit
|
commitdiff
|
tree
2014-06-09
Erik
L
i
n
dahl
Modify single/doub
l
e EP
S
t
o
agree
with ISO
C
commit
|
commitdiff
|
tree
2014-06-07
Erik Lindahl
Added
p
ackage version to
t
ng_io CMakelis
t
s
.
txt
commit
|
commitdiff
|
tree
2014-06-05
Berk H
e
ss
Fix constrain
t
vi
r
ial with multiple time stepping
commit
|
commitdiff
|
tree
2014-06-05
Mark Abraham
New quotes
commit
|
commitdiff
|
tree
2014-06-04
Rossen Apostolov
Updated C-/N-term
i
n
a
l partial charges in Amb
e
r03
.
ff
.
commit
|
commitdiff
|
tree
2014-06-03
Mark Ab
r
a
ham
Use RNG
correctly f
o
r v-rescale t
h
e
r
most
a
t
commit
|
commitdiff
|
tree
2014-06-01
Szilá
r
d Páll
Add
q
u
o
te on
t
h
e
k
T
-kj/mol conversion factor
commit
|
commitdiff
|
tree
2014-06-01
Eri
k
Lin
d
ahl
Fixed typo in manual
commit
|
commitdiff
|
tree
2014-05-31
David van der Sp
o
el
Permit trjconv t
o
read
and write v
e
loc
i
ti
e
s
w
ith T
N
G
.
.
.
commit
|
commitdiff
|
tree
2014-05-30
M
a
rk Abraha
m
F
inalize
c
hange
f
rom
GM
X
_CP
U
_ACCELER
A
TION to
G
MX_SIMD
commit
|
commitdiff
|
tree
2014-05-24
R
o
ssen Apos
t
olo
v
Simplified section "Po
r
t
i
ng"
.
commit
|
commitdiff
|
tree
2014-05-22
Ro
s
s
e
n Apo
s
to
l
o
v
Norm
a
l m
o
des don't work currently with virt
u
al sites
.
.
.
commit
|
commitdiff
|
tree
2014-05-22
Teemu Murtola
Fix static g
r
oup list in
d
i
ces in selec
t
ion prompt
commit
|
commitdiff
|
tree
2014-05-22
Berk
H
ess
A
v
oid energy
d
r
i
ft with verle
t
-buffer-t
o
lerance
commit
|
commitdiff
|
tree
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