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Added CMake Toolchain file for BlueGene/P
2012-01-04
M
ark Abraham
Add
e
d CMake Too
l
chain
fil
e
fo
r
BlueGene/
P
commit
|
commitdiff
|
tree
2011-12-14
M
a
rk Abraham
R
e
-fix
e
d static linking o
f
math
s
libraries under U
N
IX
commit
|
commitdiff
|
tree
2011-12-13
Mar
k
A
b
raham
Relaxed some assumptions
abou
t
tra
j
ectory times
commit
|
commitdiff
|
tree
2011-11-23
Mark Abraham
Fixed g_angle
-
f -
o
r to cop
y
t
i
m
e
s
from -
f
to -o
r
commit
|
commitdiff
|
tree
2011-11-02
Mark Ab
r
a
h
am
Fi
x
for G
B
,
double, SS
E
2
a
n
d o
p
timized kernels
commit
|
commitdiff
|
tree
2011-11-01
Mark Abraham
Trig
g
er correct ke
r
n
e
l
s
u
n
der C
y
gwin
commit
|
commitdiff
|
tree
2011-10-27
Mark
Abraham
Made reading of bin
a
ry matric
e
s more robust
commit
|
commitdiff
|
tree
2011-10-19
M
a
rk
Abraham
Co
r
rected charge of CHARMM
zinc
i
on
t
o +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abr
a
h
am
Remo
v
e
d erroneous
u
s
e of MA
S
SV on B
l
ueGene
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
F
ixes f
o
r GB
kernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraham
Added ti
p
for con
v
erting
.
xpm to
s
o
mething useful
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Droppe
d
some hints in th
e
d
ocumenta
t
ion
commit
|
commitdiff
|
tree
2011-09-26
M
a
rk Ab
r
aham
Removed
C
M
a
ke war
n
ing
f
or recent Ope
n
M
P
I versions
commit
|
commitdiff
|
tree
2011-09-15
Mark Ab
r
aham
Fix trjconv -sub
commit
|
commitdiff
|
tree
2011-09-15
Mar
k
Abraham
Warni
n
g
a
bout trjconv -sub
n
e
eding many files open
commit
|
commitdiff
|
tree
2011-09-15
M
ar
k
A
b
raham
g_sha
m
-m
d
ata
i
s an inp
u
t
file,
n
o
t output
file
commit
|
commitdiff
|
tree
2011-09-14
Ma
r
k Abraham
Forma
t
warn
i
ng better
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fix pdb2gmx -debu
g
and
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fix for CMake
findi
n
g LAPA
C
K
commit
|
commitdiff
|
tree
2011-09-13
Mark Ab
r
ah
a
m
Ad
d
ed ACE and
CT3 to CHARMM27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
ark
Ab
r
aham
F
i
x
e
d ch
a
rge groups of
C
H
ARMM27 DNA/RNA terminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
raham
Fi
x
e
s
for
C
M
a
ke finding FORTRAN
l
ibrary names on
P
OW
E
R
6
commit
|
commitdiff
|
tree
2011-09-06
M
a
r
k
A
b
raham
Fix
b
ug with large ints witho
u
t
MPI_IN
_
PL
A
CE
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Made gr
o
mpp no
t
e
a
bo
u
t no
n
-zero ch
a
r
g
e more
u
s
e
ful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abr
a
ham
Re-implemented generati
n
g
de
f
aul
t
protei
n
index groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Ab
r
a
h
am
Adjust
e
d cons
t
ruction
of default index gr
o
ups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abr
a
ham
Fi
x
ed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Fixed g
_
di
s
re dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
T
y
po
fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Ab
r
aham
Expl
a
ined term
i
nal
residues and AMB
E
R in pdb2gmx -h
commit
|
commitdiff
|
tree
2011-08-16
Mar
k
Abraham
Ma
d
e
f
ree en
e
rgy perturbation work with CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abraham
Fixed output bu
g
in demu
x
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Str
e
a
m
lined smal
l
part of
pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
M
ark Abraham
Reading
a
.
g96 t
r
a
je
c
t
o
r
y
n
o
w causes fatal e
r
ror
commit
|
commitdiff
|
tree
2011-07-11
Mar
k
Abraham
Fix some iden
t
ifier naming issue
s
in last commit
commit
|
commitdiff
|
tree
2011-07-11
Mark Abra
h
am
Avoided some int
e
ger over
f
lows
commit
|
commitdiff
|
tree
2011-07-08
Mark Abr
a
h
a
m
C
l
ari
f
ie
d
u
se of OPLS/AA zwitte
r
i
on
t
ermini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abr
a
ham
Fixe
d
improper
f
i
le close wit
h
GB an
d
mdrun -deb
u
g
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk Abraha
m
Mad
e
pd
b
2g
m
x error messag
e
less
c
r
y
ptic
commit
|
commitdiff
|
tree
2011-06-29
Mark
A
b
raham
Reve
r
t
"
dr
a
ft"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Improved
error mess
a
ge and docum
e
ntat
i
o
n
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
draf
t
commit
|
commitdiff
|
tree
2011-06-21
Mark Abra
h
a
m
Expand
e
d LINCS warni
n
g tex
t
commit
|
commitdiff
|
tree
2011-06-07
M
ark Abrah
a
m
F
i
xed spe
l
ling
o
f reprodu
c
ible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
A
d
ded re
f
e
r
en
c
e to g_sas -h
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Cl
e
a
n
ed
up g_sas help text
commit
|
commitdiff
|
tree
2011-05-09
Mark
A
brah
a
m
Adde
d
hint abo
u
t c
a
lling trjconv more
t
han once
commit
|
commitdiff
|
tree
2011-05-09
Mark A
b
raham
Spaced out par
a
graphs in
trjconv h
e
lp
commit
|
commitdiff
|
tree
2011-05-02
Mark Abra
h
am
Removed duplic
a
t
e
def
i
n
i
tion of md_print_
w
arnin
g
()
commit
|
commitdiff
|
tree
2011-05-01
M
ark Abraham
Fixed descript
i
on of
.
mdp opti
o
n
to "h-bond
s
"
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abraham
Removed unne
c
essary #i
n
cludes
commit
|
commitdiff
|
tree
2011-04-14
M
ark Abraham
Dele
t
ed dupli
c
at
e
d code
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved
v
ariou
s
support
functions for do
_
md into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraha
m
Moved
iterated-constraints
c
ode into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark A
b
r
a
h
a
m
Moved heuristic
n
eighbor-list
c
ode into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Ab
r
ah
a
m
Fixed
cod
e
duplic
a
tio
n
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
Fixed
header #ifn
d
ef
t
est
commit
|
commitdiff
|
tree
2011-03-30
Mark Abr
a
ham
Removed useles
s
co
n
s
t
qua
l
ifier
commit
|
commitdiff
|
tree
2011-03-30
Mark Abraham
Suppressed
C
ygwin
C-only compile
r
warnings
commit
|
commitdiff
|
tree
2011-03-26
Ma
r
k Abraham
Fixed g_cluster logic er
r
o
r
commit
|
commitdiff
|
tree
2011-03-26
Mark
Ab
r
aham
Made
gmx_rmpbc_t object funct
i
ons not s
e
gf
a
ul
t
commit
|
commitdiff
|
tree
2011-03-26
Mark
A
braham
F
ixed m
a
tio
.
c
sfre
e
() that made D
v
dS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added
g
rompp note about avoiding zero-step
EM
commit
|
commitdiff
|
tree
2011-02-16
Mark
A
b
r
aham
Clarified
source of g_rmsf r
e
f
e
r
e
n
ce frame
commit
|
commitdiff
|
tree
2011-02-13
Mark
A
braham
Added workaround for F_GB13 d
u
plicates
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraham
Fixed erroneous fl
o
a
ti
n
g-point comparis
o
n
commit
|
commitdiff
|
tree
2011-02-12
Mark
Abraham
Added note about doing repeat invocations of
genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
R
e
moved ancien
t
CVS
tag lines
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used some
s
pac
i
n
g
to make
c
ode reada
b
le
commit
|
commitdiff
|
tree
2011-02-11
Ma
r
k
A
braham
Used
sym
b
ol
i
c consta
n
t mor
e
consistently
commit
|
commitdiff
|
tree
2011-02-11
M
a
r
k
Abraham
Made the
"mul
t
i
ple s
e
t
t
le
s
" fatal error
m
ore h
e
lpful
commit
|
commitdiff
|
tree
2011-02-02
Mark Abraham
F
i
xed minor issue
w
ith r
e
plica e
x
change
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Added forgotten f
i
le
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Turned g_options into a normal G
R
OM
A
CS tool
commit
|
commitdiff
|
tree
2011-01-28
Mark
Abraha
m
Rename
d
src/tools/options
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mar
k
Abra
h
am
Improve
d
grompp
d
ocumentat
i
on
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved genion -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abrah
a
m
Relocated some t_m
a
t
r
ix documentati
o
n
commit
|
commitdiff
|
tree
2011-01-25
M
ark Abra
h
am
Imp
r
o
ved d
o
_dss
p
-ssdump output
commit
|
commitdiff
|
tree
2011-01-25
Mark Abra
h
am
Impr
o
ved do_dssp
-
sc output
commit
|
commitdiff
|
tree
2011-01-23
M
ark Abra
h
am
Remov
e
g
_
highw
a
y from list of programs
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk A
b
raham
I
mprove
d
co
n
v
ersion of
d
ocume
n
tati
o
n to LaTe
X
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Im
p
roved con
s
istency of text style usa
g
e
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
braham
Minor wording fix
e
s
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk Abraham
Mov
e
d
options
.
c to
t
o
ols subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
r
aham
cmake: add
e
d back gs
l
suppo
r
t
(
GMX_GSL, disabled
b
y
.
.
.
commit
|
commitdiff
|
tree
2011-01-23
Christoph Junghans
cmake: added GM
X
_XM
L
to fully dis
a
ble xml support
commit
|
commitdiff
|
tree
2011-01-23
Chr
i
stoph J
u
nghans
cmake: add
s
upport for exter
n
al blas/lapack
commit
|
commitdiff
|
tree
2011-01-20
M
ark Abraham
Added NHE to O
P
LS/AA p
d
b
2
gmx hydrogen d
a
t
abas
e
commit
|
commitdiff
|
tree
2011-01-20
Ma
r
k A
b
rah
a
m
M
a
d
e gmxdump error message clearer
.
commit
|
commitdiff
|
tree
2011-01-18
Mar
k
Ab
r
aham
Im
p
rov
e
d
.
mdp f
i
le comment about t
h
e 'define'
f
ield
commit
|
commitdiff
|
tree
2011-01-17
Mark
A
braham
Fix Angstr
o
m <=
>
nm error in documentation
commit
|
commitdiff
|
tree
2011-01-13
M
ar
k
Abraha
m
M
ade s
r
c
/
k
e
r
nel/repl_ex
.
c legible
commit
|
commitdiff
|
tree
2011-01-07
Mark
A
braham
A
dded n
o
te that g_msd -mo
l
d
oes treat PBC (b
y
making
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Ma
r
k Abraham
Implem
e
nte
d
effec
t
ive test for MPI_IN_PLACE, thanks
.
.
.
commit
|
commitdiff
|
tree
2011-01-06
M
a
rk
A
braham
Stop C
M
ake defaulting to tu
r
n
ing off c
o
mpil
e
r w
a
rn
i
ngs
.
.
.
commit
|
commitdiff
|
tree
2010-12-06
Mark
A
b
r
aham
Added comments
and w
o
rkarou
n
d for IBM's BlueG
e
ne(/L
.
.
.
commit
|
commitdiff
|
tree
2010-11-22
Mark
A
b
r
aham
A
dded
a
hin
t
to
t
he documen
t
a
t
ion for c
r
eati
n
g
.
tpr
.
.
.
commit
|
commitdiff
|
tree
2010-11-12
Mark
Ab
r
aham
Mi
n
or
trjconv documentation fo
r
m
a
tting
f
i
x
commit
|
commitdiff
|
tree
2010-11-12
Mar
k
A
b
rah
a
m
g_
d
ensmap -od writes
a
.
dat fi
l
e
and
pre
v
ents writing
.
.
.
commit
|
commitdiff
|
tree
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