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More editorial fixes to tool documentation
2012-03-09
M
a
rk Abraham
More editorial
f
ix
e
s to tool
doc
u
mentation
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
Edit
o
rial changes
to tool
s
documenta
t
ion
commit
|
commitdiff
|
tree
2012-02-24
Mark Abraham
Minor fo
r
ma
t
ting fixes to
.
mdp option
d
o
c
ument
a
tio
n
commit
|
commitdiff
|
tree
2012-02-23
Mark Abraham
Fix pd
b
2gmx -c
m
ap in corner cases
commit
|
commitdiff
|
tree
2012-02-10
M
a
r
k
Abra
h
am
Fixed g_sham
us
i
ng more th
a
n three dimensions
commit
|
commitdiff
|
tree
2012-02-10
Mark Abra
h
am
Integ
e
r
multiplic
a
tion that c
h
ecks f
o
r overflo
w
commit
|
commitdiff
|
tree
2012-02-01
Mark
A
b
raham
Fixed t
r
j
conv -sub
commit
|
commitdiff
|
tree
2012-02-01
Mark
Abraham
Improved error
message
commit
|
commitdiff
|
tree
2012-01-31
Mark Ab
r
aham
Ma
d
e
e
rror mes
s
age eve
n
more explicit
commit
|
commitdiff
|
tree
2012-01-31
Mark A
b
raham
C
o
rre
c
ted use of ?
:
in conditional
commit
|
commitdiff
|
tree
2012-01-10
Mark Ab
r
aham
Fixe
d
us
e
of isfin
i
te and _isfin
i
te
commit
|
commitdiff
|
tree
2012-01-04
M
a
rk Abraha
m
A
d
d
e
d
CMake To
o
lchain file fo
r
BlueGene/P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraha
m
Do
c
umented the functi
o
n of g_clus
t
er -cl -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark A
b
raham
Re-fixed s
t
atic li
n
king
o
f ma
t
h
s
l
ibrari
e
s under UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
Relaxed
some a
s
sumpti
o
ns about trajectory times
commit
|
commitdiff
|
tree
2011-11-23
Mark Abra
h
am
F
ixed g_angle -f -
o
r to copy
t
imes from -f to -o
r
commit
|
commitdiff
|
tree
2011-11-02
M
a
rk
A
braham
Fix for GB, dou
b
l
e, SSE2 and optimized ke
r
n
els
commit
|
commitdiff
|
tree
2011-11-01
Mark Abrah
a
m
T
r
i
g
g
e
r c
o
rrect ke
r
ne
l
s
unde
r
Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abraham
Made readin
g
of
b
inary matrices m
o
r
e
robust
commit
|
commitdiff
|
tree
2011-10-19
Mark
Abraham
Corrected charge
o
f CHARMM z
i
nc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Remo
v
ed erron
e
ous u
s
e of
MASSV on BlueGene
commit
|
commitdiff
|
tree
2011-10-06
Ma
r
k Abraham
Fix
e
s for GB kernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraham
Added
tip fo
r
c
o
n
v
e
rting
.
x
p
m
to so
m
ething use
f
ul
commit
|
commitdiff
|
tree
2011-09-26
Ma
r
k Abraham
Dropp
e
d
s
ome hints in the
d
ocumentation
commit
|
commitdiff
|
tree
2011-09-26
Mar
k
Abraham
Re
m
oved
C
Make warning for recent
O
penMPI versions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abra
h
am
Fix
t
r
j
conv -sub
commit
|
commitdiff
|
tree
2011-09-15
Mar
k
Abra
h
am
Warning a
b
out trjconv -
s
ub needing many fi
l
es o
p
en
commit
|
commitdiff
|
tree
2011-09-15
Mark A
b
raham
g_sham -mdata is an input file
,
not output file
commit
|
commitdiff
|
tree
2011-09-14
M
ark Abraham
F
o
rmat warning better
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraha
m
F
i
x pdb2gmx -
d
ebug an
d
.
hdb
file
s
commit
|
commitdiff
|
tree
2011-09-13
Mark
A
b
raham
Fix for CMake finding LAPACK
commit
|
commitdiff
|
tree
2011-09-13
Mark Abrah
a
m
Ad
d
ed ACE and C
T
3
t
o CHARMM27 a
m
inoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
ark Ab
r
aham
Fixed c
h
arge groups of CHARMM27 DNA
/
RNA t
e
r
m
inal H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abrah
a
m
Fixe
s
f
o
r CMake finding
FORTRAN library
n
am
e
s o
n
POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark
A
braham
F
i
x
b
u
g
with large ints
withou
t
M
P
I
_
I
N
_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Made grompp no
t
e about non-zero
c
harge more us
e
ful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Re-i
m
plemented generating default
p
rotein index
groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Adjus
t
ed c
o
nstruction of defa
u
lt index g
r
oups
commit
|
commitdiff
|
tree
2011-09-01
Mar
k
Abraham
Fixed comme
n
t
commit
|
commitdiff
|
tree
2011-08-23
Mark
Abraham
Fixe
d
g_disr
e
de
r
eferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark Abra
h
a
m
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
Explained terminal residues and AMBER in pdb2gmx -h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abraham
Made free energy
p
ertur
b
ation wor
k
with
CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark
Abra
h
am
Fix
e
d
output bug in demux
.
p
l
commit
|
commitdiff
|
tree
2011-07-17
Mark
Abraha
m
Streamlined small par
t
o
f
pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark
A
br
a
ham
Reading
a
.
g
96
trajectory now causes fat
a
l
error
commit
|
commitdiff
|
tree
2011-07-11
Ma
r
k Abraham
F
i
x some i
d
entifie
r
naming i
s
sues in last commi
t
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Avoided some
i
nte
g
er overflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Abrah
a
m
Clarified u
s
e o
f
OPLS/AA z
w
itterion termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Fixed improper
file c
l
ose with GB a
n
d mdrun -
d
ebug
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
aham
M
ade pdb2
g
mx error messag
e
l
e
ss cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Revert "draf
t
"
commit
|
commitdiff
|
tree
2011-06-29
Mark A
b
raham
I
mpr
o
ved error message and documenta
t
ion
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
dra
f
t
commit
|
commitdiff
|
tree
2011-06-21
Mar
k
Abr
a
ha
m
Expanded
L
INCS wa
r
ning text
commit
|
commitdiff
|
tree
2011-06-07
Mark
A
b
r
a
h
a
m
F
ixe
d
s
p
elli
n
g of reproduci
b
le
commit
|
commitdiff
|
tree
2011-05-11
M
a
r
k
Abraham
Adde
d
r
eference to g_sas -h
commit
|
commitdiff
|
tree
2011-05-11
Mark Abr
a
h
a
m
Cleaned up g
_
s
a
s help tex
t
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
Added h
i
nt
about calling trjconv more
t
han
once
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
Spa
c
ed o
u
t p
a
ragraphs in trjconv help
commit
|
commitdiff
|
tree
2011-05-02
Mark Abra
h
am
Removed duplicate defi
n
ition
o
f
md_print_
w
ar
n
ing
(
)
commit
|
commitdiff
|
tree
2011-05-01
M
a
r
k Abraham
Fi
x
ed descri
p
tion of
.
mdp option
to "h
-
b
o
nd
s
"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Removed u
n
ne
c
ess
a
ry #includes
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Deleted dup
l
icated code
commit
|
commitdiff
|
tree
2011-04-14
Mark Abrah
a
m
M
o
ved various s
u
pport
f
unctions for do_md
i
n
t
o
mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Ab
r
aham
M
o
ved iterated-constraints c
o
de in
t
o
mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved h
e
uris
t
ic neighbor-list code into
mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
Fixed
code duplicat
i
on
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abr
a
ham
Fix
e
d h
e
a
d
er #ifnde
f
test
commit
|
commitdiff
|
tree
2011-03-30
Mark Abr
a
h
am
Remov
e
d useless cons
t
qualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark Abraham
Supp
r
e
s
sed
Cygwin C-only compiler
warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
F
i
xed
g
_cl
u
ster logic
e
r
r
or
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Made gmx_
r
mpbc_t obje
c
t fu
n
ctions not segfaul
t
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fixed matio
.
c
sf
r
ee() that made DvdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
M
ar
k
Abraham
Added gro
m
pp
n
o
te a
b
out avoiding zero-s
t
ep EM
commit
|
commitdiff
|
tree
2011-02-16
Mark A
b
raham
Clarif
i
ed source of
g
_
rmsf reference frame
commit
|
commitdiff
|
tree
2011-02-13
Mark Ab
r
aham
Added workarou
n
d for F_GB13 duplica
t
e
s
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraha
m
F
i
xed erroneo
u
s
f
loating-point comp
a
rison
commit
|
commitdiff
|
tree
2011-02-12
Mark Abraham
Adde
d
not
e
about doing r
e
peat
invoc
a
tions of
g
enbox
commit
|
commitdiff
|
tree
2011-02-11
M
a
rk
A
brah
a
m
Removed
a
n
cient CVS
t
ag lines
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
ra
h
am
Used some spacing to
ma
k
e code readable
commit
|
commitdiff
|
tree
2011-02-11
Mark
Abraham
U
s
ed sym
b
olic cons
t
ant more
consistently
commit
|
commitdiff
|
tree
2011-02-11
Mark Abr
a
h
a
m
Made
t
h
e
"multiple sett
l
es"
f
ata
l
error more helpful
commit
|
commitdiff
|
tree
2011-02-02
Mark A
b
raham
Fixed m
i
nor
i
ssue with
r
eplic
a
excha
n
g
e
commit
|
commitdiff
|
tree
2011-01-28
M
a
rk Abraham
Ad
d
e
d
forgotten file
commit
|
commitdiff
|
tree
2011-01-28
Mark A
b
ra
h
am
Turne
d
g_op
t
ions into
a normal GROM
A
CS t
o
ol
commit
|
commitdiff
|
tree
2011-01-28
Mark
A
braham
Renamed sr
c
/tools/
o
ptions
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Improve
d
grompp documentation
commit
|
commitdiff
|
tree
2011-01-25
Mark
A
b
raha
m
Imp
r
oved ge
n
ion -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abrah
a
m
R
e
located some t_matrix documenta
t
ion
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved d
o
_
d
s
sp
-
s
s
d
u
mp outpu
t
commit
|
commitdiff
|
tree
2011-01-25
M
ark Abraham
Improv
e
d
do_dssp -sc output
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Remove
g
_
h
ighway from li
s
t of programs
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
r
a
ham
Imp
r
ove
d
c
o
nve
r
sion o
f
documentati
o
n
to LaTeX
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
I
m
p
r
o
ved consiste
n
cy of text
s
t
yle usage
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraha
m
Mi
n
o
r
wording fixes
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
raham
Moved
o
ptions
.
c to to
o
ls subdi
r
commit
|
commitdiff
|
tree
2011-01-23
Mark Abra
h
am
cm
a
k
e
: added bac
k
gsl support (GMX_GSL,
disa
b
led by
.
.
.
commit
|
commitdiff
|
tree
2011-01-23
Chris
t
op
h
J
u
ng
h
ans
cmake: adde
d
GMX_XM
L
to fully disa
b
le x
m
l suppo
r
t
commit
|
commitdiff
|
tree
2011-01-23
Christop
h
Jung
h
ans
cmake: add
su
p
port for
e
xternal blas
/
l
a
p
a
ck
commit
|
commitdiff
|
tree
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