repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Added tip for converting .xpm to something useful
2011-09-27
M
a
r
k
A
braham
Adde
d
tip for converti
n
g
.
xpm to
s
o
mething useful
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dropped s
o
me hi
n
ts in t
h
e
d
ocu
m
ent
a
tion
commit
|
commitdiff
|
tree
2011-09-26
Mark Abrah
a
m
Remov
e
d CMake warning f
o
r r
e
cent O
p
enMPI versions
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
braham
Fix trjconv -
s
ub
commit
|
commitdiff
|
tree
2011-09-15
M
ar
k
A
braham
Warning ab
o
ut t
r
j
c
onv -s
u
b needing many files ope
n
commit
|
commitdiff
|
tree
2011-09-15
Mark Abrah
a
m
g_s
h
am -mdata is a
n
inpu
t
fi
l
e
, not output file
commit
|
commitdiff
|
tree
2011-09-14
Ma
r
k Abraha
m
Fo
r
m
at warning
bette
r
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abraham
Fix pdb2g
m
x -deb
u
g
and
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mark
A
b
r
a
ham
Fix for CMake
f
ind
i
ng LAPACK
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk Abraham
Added
A
CE
and CT3 to CHARMM27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Ma
r
k Abraham
Fixed
char
g
e grou
p
s of
CHARMM27 DNA/RNA ter
m
inal H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fi
x
es fo
r
C
Make
finding FORTR
A
N
l
i
brary n
a
m
es
o
n POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraham
Fix bug wit
h
l
arge ints w
i
thout MPI_IN_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k Abraham
M
a
de grompp note about
non-zero c
h
arge mo
r
e useful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Re-implemented
g
e
nerat
i
ng
d
efault protein i
n
d
e
x groups
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k Abr
a
ha
m
Adjus
t
ed constructi
o
n
of default index grou
p
s
commit
|
commitdiff
|
tree
2011-09-01
M
ark Ab
r
ah
a
m
Fixed comm
e
nt
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Fix
e
d g_disre dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark
Abraham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
E
xplained ter
m
inal
r
esidues
an
d
AMBER in pdb2gm
x
-h
commit
|
commitdiff
|
tree
2011-08-16
M
ark Abraham
Made
fr
e
e ene
r
gy perturbation wo
r
k with CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abraham
Fixed output bu
g
in demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark A
b
raham
Stre
a
mlined small par
t
of
pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Ma
r
k Ab
r
aham
Rea
d
ing a
.
g
9
6 t
r
aject
o
ry
n
ow causes fatal er
r
or
commit
|
commitdiff
|
tree
2011-07-11
Mark Ab
r
aham
Fi
x
some identifier nam
i
ng issues in last com
m
it
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Avoided
s
ome integ
e
r overflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
aham
Clarified use
of
O
PLS/AA zwitterio
n
termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraha
m
Fixed impro
p
er fi
l
e close with GB and mdrun -debug
commit
|
commitdiff
|
tree
2011-07-08
Ma
r
k Abraham
Made
pdb
2
g
m
x error message less cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark Ab
r
aham
Rever
t
"draft
"
commit
|
commitdiff
|
tree
2011-06-29
Ma
r
k
A
b
r
aham
Improved e
r
ror message and docume
n
tation
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
dra
f
t
commit
|
commitdiff
|
tree
2011-06-21
Mark Abraham
Expanded LINCS warning text
commit
|
commitdiff
|
tree
2011-06-07
Mar
k
Abraham
Fixed spelling of reproducible
commit
|
commitdiff
|
tree
2011-05-11
M
a
rk Abraha
m
Adde
d
reference
t
o g_sas
-
h
commit
|
commitdiff
|
tree
2011-05-11
Mark A
b
r
a
ham
Cleaned up g
_
sas help text
commit
|
commitdiff
|
tree
2011-05-09
Mark Ab
r
aham
Added
h
in
t
about callin
g
trjconv more than once
commit
|
commitdiff
|
tree
2011-05-09
Mark Ab
r
aham
Spaced ou
t
p
a
r
agraphs in trjconv help
commit
|
commitdiff
|
tree
2011-05-02
Mark Abraham
R
e
m
o
ved du
p
lic
a
te defin
i
t
i
o
n
o
f
md
_
print_warning()
commit
|
commitdiff
|
tree
2011-05-01
M
a
rk
Abraha
m
Fixed description of
.
mdp option t
o
"h-bonds
"
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
br
a
ham
Re
m
oved unnecess
a
ry #includes
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Deleted d
u
p
licated code
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Ab
r
aham
Moved v
a
ri
o
u
s
support functions for do_md
into mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
ark
Abraham
M
oved iterat
e
d-
c
o
n
straints code into mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
ark
A
b
raham
Moved heuristic ne
i
ghbor-list cod
e
into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed cod
e
duplicat
i
on
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed header #ifndef test
commit
|
commitdiff
|
tree
2011-03-30
Mark Abraham
Removed useless
c
onst q
u
alifier
commit
|
commitdiff
|
tree
2011-03-30
M
ark Abraha
m
S
upp
r
e
ssed Cygwin C-o
n
ly co
m
p
i
ler warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fixed
g_cluster logic error
commit
|
commitdiff
|
tree
2011-03-26
M
a
rk Abraham
Made gmx_rmpbc_t object functions
n
ot segfault
commit
|
commitdiff
|
tree
2011-03-26
M
a
rk Abraham
F
i
xed ma
t
io
.
c
sfree() that made
DvdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark A
b
rah
a
m
Added grompp not
e
abo
u
t avoiding zer
o
-step EM
commit
|
commitdiff
|
tree
2011-02-16
Mark Abraham
Clarif
i
e
d
sour
c
e of g
_
r
m
sf re
f
erence fra
m
e
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraham
Added workaro
u
nd for F_GB13 d
u
plicates
commit
|
commitdiff
|
tree
2011-02-13
Mar
k
Abraham
Fixed erro
n
eous
fl
o
ating-point compa
r
i
s
on
commit
|
commitdiff
|
tree
2011-02-12
Mark Abraham
Added note about do
i
ng re
p
e
at invo
c
ations
of
genb
o
x
commit
|
commitdiff
|
tree
2011-02-11
Mark Ab
r
aham
Remo
v
e
d ancient CVS tag lines
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
raha
m
Used so
m
e sp
a
c
i
n
g
to make
cod
e
read
a
ble
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used s
y
mbolic
cons
t
ant mo
r
e consis
t
e
n
tly
commit
|
commitdiff
|
tree
2011-02-11
Ma
r
k Abra
h
am
Ma
d
e the "multiple
s
ettle
s
" fatal error
m
ore helpful
commit
|
commitdiff
|
tree
2011-02-02
Mark
A
braham
Fix
e
d minor i
s
sue
with re
p
lica exchange
commit
|
commitdiff
|
tree
2011-01-28
Mar
k
Abraham
Added
f
orgotten
file
commit
|
commitdiff
|
tree
2011-01-28
Mark Abra
h
am
T
urne
d
g
_
option
s
into
a no
r
mal GROM
A
CS tool
commit
|
commitdiff
|
tree
2011-01-28
Mark Abrah
a
m
Rena
m
ed src
/
tool
s
/options
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mar
k
Abraham
Improved gromp
p
documentation
commit
|
commitdiff
|
tree
2011-01-25
Mark
Abraham
Improved genion -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Rel
o
cated some
t
_
m
atrix doc
u
mentation
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved do_d
s
sp -ssdu
m
p output
commit
|
commitdiff
|
tree
2011-01-25
Mark Abrah
a
m
Improved do
_
dssp -sc output
commit
|
commitdiff
|
tree
2011-01-23
Mark Ab
r
aham
Remove g_
h
ighway from list of programs
commit
|
commitdiff
|
tree
2011-01-23
M
a
r
k Abraha
m
Improved c
o
n
version of
d
o
cumenta
t
i
o
n to La
T
eX
commit
|
commitdiff
|
tree
2011-01-23
Mar
k
Abraham
Impr
o
ved consisten
c
y of text style usage
commit
|
commitdiff
|
tree
2011-01-23
Mark Abrah
a
m
Minor wordi
n
g fixe
s
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
ra
h
am
Moved op
t
ions
.
c
t
o tools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
br
a
ha
m
c
make:
a
dded back
gsl support
(
G
M
X_GSL, disab
l
ed by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
M
ark A
b
r
ah
a
m
Added N
H
E
t
o
O
P
LS/AA
p
db2gmx hydrogen
d
a
t
a
base
commit
|
commitdiff
|
tree
2011-01-20
Mark Abraham
Made
g
mxdump
error message
c
le
a
r
e
r
.
commit
|
commitdiff
|
tree
2011-01-18
Ma
r
k Abraham
Improved
.
md
p
file comment about t
h
e
'defi
n
e'
field
commit
|
commitdiff
|
tree
2011-01-17
Mark
A
b
r
aham
Fix Angstrom
<=> nm error in do
c
umen
t
ation
commit
|
commitdiff
|
tree
2011-01-13
Mark Abraham
Made s
r
c/ke
r
nel/r
e
pl_ex
.
c legib
l
e
commit
|
commitdiff
|
tree
2011-01-07
Ma
r
k
A
b
r
ah
a
m
Added no
t
e
that g_msd -mol does treat PBC (by making
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Mark Abraham
Implem
e
nted effective tes
t
for MPI_IN_PLACE, thanks
.
.
.
commit
|
commitdiff
|
tree
2011-01-06
Mark Abraham
Stop CMake defaul
t
in
g
to
t
u
rn
i
ng o
f
f
co
m
piler warnings
.
.
.
commit
|
commitdiff
|
tree
2010-12-06
Mark
Abraham
Added com
m
e
n
ts and worka
r
ound for IBM's Blu
e
Gene(/L
.
.
.
commit
|
commitdiff
|
tree
2010-11-22
Mar
k
Ab
r
aham
Added a hin
t
to the docu
m
entation for
crea
t
i
n
g
.
tpr
.
.
.
commit
|
commitdiff
|
tree
2010-11-12
Mark Abrah
a
m
Minor
t
r
j
c
o
nv documentation
f
o
rmatting fix
commit
|
commitdiff
|
tree
2010-11-12
Mark Ab
r
ah
a
m
g_densmap -od writes a
.
dat
fi
l
e and prevents writin
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Mark Ab
r
aham
GMX_POWERPC_INV
S
QRT should be
O
FF in CMakeLists
.
txt
.
.
.
commit
|
commitdiff
|
tree
2010-11-07
Mark
A
b
r
aham
Made mdrun exit with a f
a
tal e
r
ror for EM
or NM
w
i
th
.
.
.
commit
|
commitdiff
|
tree
2010-11-06
M
a
rk Abraham
Fix
e
d
.
xv
g
legends for g_s
a
s options -
o
r
and -oa
commit
|
commitdiff
|
tree
2010-10-24
M
ark Abraham
D
on't s
p
rintf var
i
a
b
l
e-sized input into f
i
x
ed-size
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark Abraham
Re-
e
nabled for BlueGene/L an opti
m
izati
o
n
i
n t
h
e
BG
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
M
ark Abraham
Rearranged c
m
a
k
e+B
l
ueGene so
l
ution
t
o
have the s
a
me
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
M
a
rk A
b
raham
Made GMX_P
O
WERPC_
I
NVSQRT work properl
y
on Power6
a
nd
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark
A
b
r
aham
P
ower6 F
O
RTR
A
N kernels
d
o not work on
P
PC4
4
0 or PPC4
5
0
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark Abraham
Fix
i
n
g
a tri
v
ial mangle int
r
oduce
d
i
n
b5d842ff1d
9
4174b6e7012
.
.
.
commit
|
commitdiff
|
tree
2010-10-20
Mark
A
braham
Fi
x
e
d cmake to
w
ork with BlueGene/L
.
This fix does
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Mark Abraham
Fix manu
a
l refere
n
ces for 'continuation'
,
rath
e
r than
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Mark Abraha
m
mk_dlist() ch
a
n
ge
d
it
s
parameter list, so its declaration
.
.
.
commit
|
commitdiff
|
tree
next