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draft
2011-06-29
M
ark A
b
r
aham
draft
commit
|
commitdiff
|
tree
2011-06-21
Mark Abraham
E
xpa
n
d
e
d LINCS w
a
rning
t
ext
commit
|
commitdiff
|
tree
2011-06-07
Mark Abraham
F
ixed
s
p
e
l
l
i
ng of
re
p
roducibl
e
commit
|
commitdiff
|
tree
2011-05-11
Ma
r
k
Abraham
Added
r
efe
r
enc
e
to
g
_
sa
s
-h
commit
|
commitdiff
|
tree
2011-05-11
M
a
rk Abraham
Clea
n
ed u
p
g_sas hel
p
text
commit
|
commitdiff
|
tree
2011-05-09
Mark Abra
h
am
Add
e
d hint
a
b
out calling t
r
j
conv
m
ore
t
han once
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Ab
r
aham
S
pace
d
out par
a
grap
h
s in trjc
o
n
v
help
commit
|
commitdiff
|
tree
2011-05-02
Ma
r
k Abraham
Remov
e
d
duplicate defin
i
tion of md_print_wa
r
n
ing()
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraham
Fixed
d
escriptio
n
of
.
mdp option to "h-
b
onds"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Remov
e
d
u
n
necessary #includes
commit
|
commitdiff
|
tree
2011-04-14
Mark Abr
a
ham
Deleted duplicated code
commit
|
commitdiff
|
tree
2011-04-14
Mark
Abraham
Moved
vario
u
s
support func
t
i
o
ns for do_md
i
nto mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abr
a
ham
Moved
iterated-constrai
n
t
s code into
mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
ark Abraha
m
Moved heuri
s
tic nei
g
hbor-list code
in
t
o mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed code duplication
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed
header #ifnde
f
test
commit
|
commitdiff
|
tree
2011-03-30
Mark
A
braham
Removed usele
s
s const qualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark
A
braham
S
uppr
e
ssed Cygwin C-on
l
y
compiler warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fixed
g_cluster logic error
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraha
m
Made gmx_r
m
pbc
_
t
o
bject
f
unctio
n
s not
s
e
gf
a
ult
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fi
x
ed matio
.
c s
f
ree() that made Dv
d
S cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Ab
r
aham
A
d
ded gro
m
pp note
a
bo
u
t avoi
d
ing ze
r
o
-step EM
commit
|
commitdiff
|
tree
2011-02-16
Mark Abra
h
am
C
l
a
r
ified sou
r
c
e
of g_rm
s
f referen
c
e frame
commit
|
commitdiff
|
tree
2011-02-13
Mark Abra
h
am
A
d
ded w
o
rkaround for
F_GB13 duplicat
e
s
commit
|
commitdiff
|
tree
2011-02-13
Ma
r
k A
b
ra
h
am
F
i
xe
d
erroneous
f
lo
a
ting-point com
p
arison
commit
|
commitdiff
|
tree
2011-02-12
Mark Abr
a
ham
Added note about doing rep
e
a
t
invoc
a
t
i
o
ns of
genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark Ab
r
ah
a
m
Removed ancient C
V
S
t
ag li
n
es
commit
|
commitdiff
|
tree
2011-02-11
Mark
A
braham
Used so
m
e sp
a
cing t
o
make code read
a
ble
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used symb
o
l
i
c constant more consis
t
entl
y
commit
|
commitdiff
|
tree
2011-02-11
Mark
Abraham
Made the
"m
u
ltiple set
t
les" fat
a
l
erro
r
more helpful
commit
|
commitdiff
|
tree
2011-02-02
Mark Abra
h
am
Fixed
m
inor i
s
sue with replica exchan
g
e
commit
|
commitdiff
|
tree
2011-01-28
Mark Abra
h
am
Added forgotten
file
commit
|
commitdiff
|
tree
2011-01-28
Mark Abra
h
am
Turned g_options into a normal
G
R
OMA
C
S t
o
ol
commit
|
commitdiff
|
tree
2011-01-28
M
a
r
k
Abraham
Renamed src/tools
/
optio
n
s
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Imp
r
oved grompp
documentatio
n
commit
|
commitdiff
|
tree
2011-01-25
M
ark Abraham
Improved
ge
n
ion -
h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
R
elocated some t_m
a
tri
x
documentation
commit
|
commitdiff
|
tree
2011-01-25
Mar
k
Abraham
Improved
do_dssp -ss
d
ump output
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved
d
o_ds
s
p
-sc output
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
b
ra
h
a
m
R
e
move g_hig
h
way from
l
ist of p
r
ograms
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
I
m
pro
v
ed c
o
n
version of docum
e
ntation
to LaTeX
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraha
m
Improved co
n
sistency of t
e
xt style usage
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
braham
Minor wording fixes
commit
|
commitdiff
|
tree
2011-01-23
Mark
Abraham
Move
d
options
.
c t
o
tools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
raham
cmake: add
e
d back
gsl suppor
t
(GM
X
_GSL, disabled by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
Mark Abraham
A
dded NHE t
o
OP
L
S
/AA pdb2gmx h
y
drogen d
a
t
abase
commit
|
commitdiff
|
tree
2011-01-20
Mark Abrah
a
m
Made gm
x
dump
e
r
ror
m
essage cleare
r
.
commit
|
commitdiff
|
tree
2011-01-18
Mark Abraham
Im
p
ro
v
ed
.
mdp f
i
le comment abou
t
the 'define'
f
ield
commit
|
commitdiff
|
tree
2011-01-17
Mark
Abraham
Fix Angstrom <=> nm
er
r
or in documentation
commit
|
commitdiff
|
tree
2011-01-13
Ma
r
k Ab
r
aham
Made sr
c
/kernel/re
p
l_ex
.
c leg
i
ble
commit
|
commitdiff
|
tree
2011-01-07
Mark Abr
a
ham
Adde
d
note that g_msd -
m
ol does trea
t
PBC (b
y
m
aking
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Mark Abraham
Implemented eff
e
ctive test for
M
PI_IN_
P
L
ACE,
thanks
.
.
.
commit
|
commitdiff
|
tree
2011-01-06
M
a
r
k Abraham
Stop CMake defaulting to turnin
g
o
ff compiler w
a
rn
i
ngs
.
.
.
commit
|
commitdiff
|
tree
2010-12-06
Mark Abrah
a
m
A
d
ded comm
e
n
t
s
an
d
workaround for IBM's BlueG
e
ne
(
/L
.
.
.
commit
|
commitdiff
|
tree
2010-11-22
Mark
Abraham
Added a h
i
nt t
o
t
h
e documentat
i
on for
c
reating
.
tpr
.
.
.
commit
|
commitdiff
|
tree
2010-11-12
M
a
r
k
A
b
raham
Minor trjconv doc
u
me
n
tat
i
on form
a
tting fix
commit
|
commitdiff
|
tree
2010-11-12
Mark Abraham
g
_
d
ensmap
-od writes a
.
dat file and
prevents wri
t
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Mark Abr
a
ham
GMX
_
P
O
W
ERPC_I
N
VSQRT
should be OFF in CMake
L
is
t
s
.
txt
.
.
.
commit
|
commitdiff
|
tree
2010-11-07
Mark Abr
a
ham
Made mdrun exit with
a
f
a
tal error fo
r
EM or NM with
.
.
.
commit
|
commitdiff
|
tree
2010-11-06
Mark Abraham
Fixed
.
x
v
g
legends for g_sas opti
o
ns -or and
-
oa
commit
|
commitdiff
|
tree
2010-10-24
Mark Abraham
Don't
sprintf variable-sized inpu
t
int
o
fixed-size
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
M
ark Abraham
Re-
e
nabled
f
or Bl
u
eGene/L
an optim
i
zation in
t
he BG
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Ma
r
k Abraham
Re
a
rrang
e
d
c
make
+
Blu
e
Gene s
o
lution to have the
same
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark Abraham
Made
G
MX_POWE
R
PC_INVSQ
R
T
work pro
p
erl
y
on
Po
w
er6
a
nd
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark Abra
h
am
Power6
F
ORTRA
N
kernels do not work
o
n PPC440 or
P
PC4
5
0
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark
A
brah
a
m
F
ixing a t
r
ivial mangle introduced in b5d
8
42
f
f1d941
7
4b6
e
701
2
.
.
.
commit
|
commitdiff
|
tree
2010-10-20
Mark Abraham
Fixed c
m
a
k
e to work
w
ith BlueGene/L
.
This fix does
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Mark Abraham
Fix manual referen
c
es
for 'contin
u
ation',
r
ather than
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Mark Abr
a
ham
mk_dli
s
t() changed its parameter list
,
so its declaration
.
.
.
commit
|
commitdiff
|
tree
2010-09-23
Mark Abraham
Fi
x
es for g_chi fo
r
bugzilla 569, so t
h
at it now uses
.
.
.
commit
|
commitdiff
|
tree
2010-09-23
M
ark Ab
r
aham
Extensions
to
th
e
gmx_residue
t
ypes_t AP
I
to meet th
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Mark A
b
rah
a
m
Wh
e
n grompp failed
t
o find the
forcefield, the error
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
M
a
rk Abraham
Formatting fixes to document
a
tio
n
commit
|
commitdiff
|
tree
2010-09-09
Ma
r
k
Abraham
A
d
ded TIP5
p
t
o CHARMM forcefield by
a
na
l
ogy with
A
M
B
ER0
3
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
M
ar
k
Abra
h
am
Spelling fix
commit
|
commitdiff
|
tree
2010-09-08
Mark Abraham
Added
n
ote to g_covar about mem
o
ry cos
t
s and mana
g
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-09-02
Mark Abraham
F
i
x spel
l
i
ng er
r
or
commit
|
commitdiff
|
tree
2010-09-01
Mark Abraham
Formatting fixes to
d
oc
u
menta
t
i
o
n
commit
|
commitdiff
|
tree
2010-09-01
Mark Abraham
Merge branch 'rel
e
ase-4-5-pa
t
ches'
o
f git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Mark Abra
h
am
m
ake_opt
.
h
tml now doesn't
u
se <h4>, rathe
r
it uses
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Mark Abr
a
ha
m
General
f
i
x
es
commit
|
commitdiff
|
tree
2010-08-30
Mark Abraham
M
a
de a pdb2gmx message less cry
p
tic wh
e
n it finds
m
ul
t
ip
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Mark A
b
rah
a
m
Sp
e
lling
f
ix
e
s in pdb2g
m
x documentation
commit
|
commitdiff
|
tree
2010-08-26
Mark Abraha
m
Made the des
c
ription
o
f
ld_seed and
gen_seed
seed
generation
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Mar
k
Abr
a
ham
Fixed
H
TML documentation to use prope
r
'&
g
e
', no
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Mark Abraham
Clarified documenta
t
io
n
ab
o
ut when gen_v
e
l gene
r
ates
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Mark Abraham
Fixed leak from unclose
d
d
irectory handle
s
when
pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Mark Abraham
Made pdb2
g
mx
b
e sligh
t
ly more he
l
pful
wh
e
n
using AMBER
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Mark
Abraha
m
Two spelling fixes in comment and output
commit
|
commitdiff
|
tree
2010-06-24
Ma
r
k Abraha
m
Added sne
w
_aligned
a
nd sfre
e
_
a
li
g
ned for managing n
.
.
.
commit
|
commitdiff
|
tree