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Continuing to fix threading on Cygwin
2012-05-26
M
a
r
k Abraham
Continu
i
ng
to fix
th
r
eading
on Cygwin
commit
|
commitdiff
|
tree
2012-04-28
Mark Abraham
Merge "Remove checks based on Generator" into rele
a
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Mark Abrah
a
m
Merge "Fix v
e
rsion info gene
r
ation for autoconf
.
" int
o
.
.
.
commit
|
commitdiff
|
tree
2012-04-19
Mark
A
braham
V
arious i
m
prov
e
ments to shel
l
code
commit
|
commitdiff
|
tree
2012-04-14
Mar
k
Abraham
D
escribed default o
u
tput be
h
aviour
commit
|
commitdiff
|
tree
2012-04-14
Mark Ab
r
aham
Clarified warning messa
g
e
commit
|
commitdiff
|
tree
2012-04-14
Mark
A
bra
h
am
Clarifie
d
war
n
ing str
i
ng
commit
|
commitdiff
|
tree
2012-04-10
Mar
k
Abraham
Ma
d
e g_helix sensitive to C
H
ARMM atom nami
n
g
commit
|
commitdiff
|
tree
2012-04-10
Ma
r
k Abr
a
ham
Permit threads
bui
l
d o
n
Cygw
i
n
commit
|
commitdiff
|
tree
2012-04-09
Mark
Abraham
Docu
m
entation and error message enhanc
e
ments
commit
|
commitdiff
|
tree
2012-04-09
M
a
rk Abraham
Lots of manual updates
commit
|
commitdiff
|
tree
2012-04-09
M
ark Abrah
a
m
Consolidated documenta
t
ion of
.
m
dp restra
i
nt options
commit
|
commitdiff
|
tree
2012-04-02
Mar
k
Abraham
I
m
proved pdb2gmx e
r
r
o
r m
e
ssag
e
commit
|
commitdiff
|
tree
2012-04-02
Mark Abra
h
am
Keep CMak
e
quiet
a
b
o
ut a
Cygwin issue
commit
|
commitdiff
|
tree
2012-03-18
Mark
A
b
raham
Warnings a
g
ains
t
equilibratin
g
with P-R P-coupling
commit
|
commitdiff
|
tree
2012-03-15
Ma
r
k
Abr
a
ham
Clarified wording of documentatio
n
commit
|
commitdiff
|
tree
2012-03-14
Ma
r
k
Abraham
Change
d
cr
y
ptic error message
s
about disk
quota
commit
|
commitdiff
|
tree
2012-03-09
Ma
r
k
A
braham
More e
d
it
o
r
ial fixes to too
l
documentation
commit
|
commitdiff
|
tree
2012-03-09
M
a
rk Abraham
E
d
itor
i
al changes to tools do
c
umentation
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraham
I
mproved war
n
ing n
o
te
w
it
h
D
D
and periodic molecul
e
s
commit
|
commitdiff
|
tree
2012-03-08
Mark
Abraham
Made
d
escriptio
n
string for g_s
e
l
ect -sel
e
ct clearer
commit
|
commitdiff
|
tree
2012-03-08
M
ark
A
b
r
aham
Impro
v
ed cryptic er
r
or
message
commit
|
commitdiff
|
tree
2012-02-24
M
a
rk
A
braham
Minor
formatting
f
i
xes
t
o
.
mdp
o
pt
i
o
n d
o
cum
e
n
t
at
i
on
commit
|
commitdiff
|
tree
2012-02-23
Mark Abraham
Fix
p
db2gmx -cmap i
n
corn
e
r
cases
commit
|
commitdiff
|
tree
2012-02-10
Mark Abraham
Fixed
g
_sham using
more tha
n
three di
m
ensions
commit
|
commitdiff
|
tree
2012-02-10
Mark Abraham
Integer multiplication that checks for overfl
o
w
commit
|
commitdiff
|
tree
2012-02-01
Mark Abraham
Fixed
t
rjco
n
v -sub
commit
|
commitdiff
|
tree
2012-02-01
Mark
A
braham
Fixed er
r
or message t
o
identify the correct f
i
l
e
commit
|
commitdiff
|
tree
2012-02-01
Ma
r
k
A
braham
I
mprove
d
error messa
g
e
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abraham
Merge
"
C
o
rrected use of ?: in conditional"
into relea
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Made er
r
or me
s
sage even
more explicit
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Corr
e
cted use of ?: in condi
t
ional
commit
|
commitdiff
|
tree
2012-01-10
Mark Abraham
Fixed use of isfinite and
_isfinite
commit
|
commitdiff
|
tree
2012-01-04
Mark A
b
raham
Added CMak
e
Toolc
h
ain fi
l
e for
Blu
e
Ge
n
e
/
P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraham
Documented the f
u
nct
i
on
o
f g_cluster
-
cl -no
a
v
commit
|
commitdiff
|
tree
2011-12-14
Mark
A
b
rah
a
m
Re-fi
x
ed static lin
k
ing of m
a
ths libraries unde
r
UN
I
X
commit
|
commitdiff
|
tree
2011-12-13
M
ark Abraham
Relaxed some
a
ssumpt
i
ons about traje
c
tory times
commit
|
commitdiff
|
tree
2011-11-24
M
ar
k
Abr
a
ham
Onl
y
ana
l
yse
a
ngle
t
ra
n
siti
o
n
s
for dihe
d
ral angl
e
s
commit
|
commitdiff
|
tree
2011-11-24
Mark
A
braham
Added protective preprocessor direc
t
ives
commit
|
commitdiff
|
tree
2011-11-23
Mark Abraham
Fix
e
d
g_an
g
le
-f -or
t
o
copy times f
r
om -f to -or
commit
|
commitdiff
|
tree
2011-11-02
M
ark Abraham
Fix for GB,
double
,
SSE2 and o
p
timize
d
k
e
rnels
commit
|
commitdiff
|
tree
2011-11-01
M
a
rk A
b
raham
T
rigger
c
orrect kernels under Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mar
k
Ab
r
aham
M
ade reading of b
i
n
ary matrices more r
o
bust
commit
|
commitdiff
|
tree
2011-10-19
M
ar
k
Abraha
m
Correc
t
ed charge of CHARMM zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark
Abraham
Removed erroneous use of MASSV o
n
BlueG
e
ne
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Fixes for GB kerne
l
commit
|
commitdiff
|
tree
2011-09-27
M
a
rk Abra
h
am
A
d
ded ti
p
fo
r
co
n
verting
.
xpm t
o
some
t
hi
n
g usef
u
l
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dropped some hints in the
d
ocumentat
i
on
commit
|
commitdiff
|
tree
2011-09-26
M
a
r
k
A
b
r
aham
Remove
d
CMake w
a
r
ning for recent Open
M
PI
versions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Fix trjco
n
v -s
u
b
commit
|
commitdiff
|
tree
2011-09-15
Ma
r
k Abrah
a
m
Warning about trjconv -
s
ub needing m
a
ny files
open
commit
|
commitdiff
|
tree
2011-09-15
M
a
rk Abraha
m
g_sha
m
-mdata is an input file, not
o
utput file
commit
|
commitdiff
|
tree
2011-09-14
Mark Abraham
Format warni
n
g bet
t
er
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk Abrah
a
m
F
i
x pdb2gmx
-
debug
and
.
h
db
f
iles
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fix for
C
Ma
k
e f
i
n
d
ing LAPACK
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abraham
Ad
d
ed
A
CE and CT3 to CH
A
R
M
M27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Ma
r
k Abr
a
ham
F
ixed charge group
s
o
f
CHARMM27
D
N
A
/RNA termina
l
H
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
r
aham
F
i
xes f
o
r
C
M
ake
f
i
ndi
n
g FORTRAN
l
ibrary names on POWE
R
6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abra
h
am
Fix bug with
la
r
g
e
i
n
ts w
i
tho
u
t
MPI_IN_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Mark A
b
raham
M
ade g
r
ompp n
o
te about no
n
-zer
o
cha
r
ge more use
f
ul
commit
|
commitdiff
|
tree
2011-09-01
Mark Abr
a
h
am
R
e
-impl
e
mented gen
e
ra
t
ing defa
u
lt protein ind
e
x g
r
oups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
A
djusted
c
onstruction
o
f default index groups
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k Abraham
Fixed
comment
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Fixed g_disre deref
e
r
encing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
M
ar
k
Abraham
Ex
p
laine
d
terminal r
e
sidues
a
nd
A
MBE
R
in pdb2gm
x
-h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abraham
M
ade
f
ree e
n
e
r
gy perturbation work with
CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abrah
a
m
Fixed
o
u
tput bug in demu
x
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abr
a
ha
m
S
treamlined s
m
al
l
p
a
r
t
of p
d
b2gmx
commit
|
commitdiff
|
tree
2011-07-15
M
a
r
k
Abrah
a
m
Reading
a
.
g96
t
r
ajecto
r
y
now causes fatal error
commit
|
commitdiff
|
tree
2011-07-11
Mar
k
Abraham
Fix some identifi
e
r
nami
n
g issues in last commit
commit
|
commitdiff
|
tree
2011-07-11
M
a
rk
A
braham
Avoide
d
some integer ov
e
rflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Clari
f
i
ed use o
f
O
PLS
/
AA zwitterion
t
e
rmini
commit
|
commitdiff
|
tree
2011-07-08
M
a
r
k
Abraham
Fixed improper file clos
e
w
ith
G
B and mdrun -debug
commit
|
commitdiff
|
tree
2011-07-08
Ma
r
k Ab
r
aham
M
a
d
e p
d
b2gmx error message less
c
ryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark Abr
a
ham
R
e
vert "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Imp
r
o
v
ed error mes
s
age and
documenta
t
i
o
n
commit
|
commitdiff
|
tree
2011-06-29
Mark A
b
r
a
h
am
draft
commit
|
commitdiff
|
tree
2011-06-21
M
ark Abraham
Exp
a
n
ded LINCS warning
tex
t
commit
|
commitdiff
|
tree
2011-06-07
Mar
k
Abr
a
ham
Fixed s
p
ell
i
ng o
f
reproducible
commit
|
commitdiff
|
tree
2011-05-11
Mark A
b
raham
Added
r
eference to g_sas
-
h
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Cleaned up g_sas help t
e
xt
commit
|
commitdiff
|
tree
2011-05-09
Mark
A
br
a
ham
Add
e
d hint a
b
out calling trjconv
more t
h
a
n
once
commit
|
commitdiff
|
tree
2011-05-09
M
a
rk Abraham
Sp
a
c
ed out parag
r
a
p
hs
i
n t
r
jconv
h
elp
commit
|
commitdiff
|
tree
2011-05-02
Mark
Abrah
a
m
Remo
v
ed
dupli
c
ate defi
n
ition of md_print_warning()
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraham
F
ixed
d
e
scriptio
n
of
.
mdp opt
i
on to "h-bonds"
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abrah
a
m
Rem
o
ved unnece
s
sary #includes
commit
|
commitdiff
|
tree
2011-04-14
Mar
k
Abrah
a
m
Deleted duplicated
c
ode
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved va
r
ious s
u
p
port functio
n
s for do_md into mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
a
r
k
Abraham
Moved iterat
e
d-
c
on
s
tra
i
nt
s
code
i
nto
mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved heuristic neig
h
bor-list
c
o
de into mdli
b
commit
|
commitdiff
|
tree
2011-04-14
M
a
r
k
Abraham
F
i
x
ed code duplic
a
t
i
on
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Ab
r
aham
Fi
x
ed header #ifndef tes
t
commit
|
commitdiff
|
tree
2011-03-30
M
ar
k
Abraham
Removed usel
e
ss const
q
ualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark Ab
r
aham
Su
p
pr
e
ssed Cygwin C-o
n
ly compiler warnin
g
s
commit
|
commitdiff
|
tree
2011-03-26
Mark Abra
h
am
Fixed g_cluster logi
c
error
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Made
g
m
x_rmpbc_t object function
s
not se
g
fa
u
l
t
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
F
i
xed matio
.
c
s
free(
)
that made D
v
dS
c
r
y
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added gro
m
pp n
o
t
e
a
bout
a
voiding z
e
ro-s
t
ep EM
commit
|
commitdiff
|
tree
2011-02-16
Mark Abraham
Cla
r
ified s
o
urc
e
of
g
_rmsf reference f
r
ame
commit
|
commitdiff
|
tree
next