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4.5.7 release
2013-04-19
Mark Abraha
m
4
.
5
.
7 release
commit
|
commitdiff
|
tree
2013-04-19
M
i
ch
a
el S
h
irts
S
o
me changes for md-vv
e
x
t
rac
t
ed fr
o
m
4
.
6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Bump sh
a
r
e
d object
v
ersion
t
o
7
commit
|
commitdiff
|
tree
2013-01-15
Mark
Abraham
Added check
for valid wall_atomtype in
.
mdp
commit
|
commitdiff
|
tree
2013-01-14
Mark Abr
a
ham
Ad
d
ed fatal
e
rror for cons
t
raints + L-B
F
GS
min
i
mizer
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Updated
co
d
e checks with distance re
s
tr
a
ints
commit
|
commitdiff
|
tree
2013-01-13
Mark
Abraham
Fixing trjconv -sub
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
N
oting that and why gmxdump
-
s -sys is broken
commit
|
commitdiff
|
tree
2012-09-24
Mark Abrah
a
m
Fix RE
M
D use o
f
g
m
x
_large_
i
nt_
t
for
#
steps variable
commit
|
commitdiff
|
tree
2012-09-10
M
ark Abraham
Cor
r
ec
t
ed
R
EMD citation
commit
|
commitdiff
|
tree
2012-08-31
Mar
k
Ab
r
aham
Improved pdb2gmx output
commit
|
commitdiff
|
tree
2012-08-28
M
ark
A
braham
Do
c
u
men
t
correc
t
co
m
m_mode
option
commit
|
commitdiff
|
tree
2012-08-10
M
ar
k
A
b
r
a
ham
A
dded TIP4P back into
C
HA
R
MM27
commit
|
commitdiff
|
tree
2012-06-15
M
ark Abraham
Quie
t
linker on Blu
e
Gene
commit
|
commitdiff
|
tree
2012-06-15
Mark
Abraham
Fix
g
_lie
c
ounting last frame twice
commit
|
commitdiff
|
tree
2012-06-06
Mark
A
braham
Work around fail
u
re of endianness testing on BlueG
e
n
e
commit
|
commitdiff
|
tree
2012-06-06
Ma
r
k
Ab
r
aham
Fix endian tes
t
functionality
commit
|
commitdiff
|
tree
2012-06-04
M
ark Abraham
Added more suggeste
d
strat
e
gies to e
r
ror m
e
ssage
commit
|
commitdiff
|
tree
2012-05-31
Mark Abraham
Ma
d
e
mdrun more ver
b
ose about PME split
commit
|
commitdiff
|
tree
2012-05-26
Mark
Abraham
Continuing
t
o
fix thread
i
n
g o
n
Cygwin
commit
|
commitdiff
|
tree
2012-04-19
Ma
r
k
Abr
a
ham
V
a
rious impr
o
vements
to shell code
commit
|
commitdiff
|
tree
2012-04-14
Mark A
b
rah
a
m
Describ
e
d defa
u
lt ou
t
put beha
v
iour
commit
|
commitdiff
|
tree
2012-04-14
M
a
rk Abraham
Clarified warni
n
g message
commit
|
commitdiff
|
tree
2012-04-14
Mark
Abraham
Clarified
w
arnin
g
s
tring
commit
|
commitdiff
|
tree
2012-04-10
M
a
rk Ab
r
a
h
am
Ma
d
e g_helix sen
s
i
t
i
v
e
to CHARMM
a
t
o
m na
m
ing
commit
|
commitdiff
|
tree
2012-04-10
Mar
k
Ab
r
aham
Pe
r
m
i
t thre
a
ds build on
C
y
gwin
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraha
m
D
ocumentation and error message en
h
ancements
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraham
Lots of manua
l
updates
commit
|
commitdiff
|
tree
2012-04-09
Ma
r
k
Abraham
Cons
o
lidated documentation
o
f
.
mdp restraint options
commit
|
commitdiff
|
tree
2012-04-02
Mark Abraham
Impr
o
ved pdb2gmx error message
commit
|
commitdiff
|
tree
2012-04-02
Ma
r
k Abraham
Keep
CMake quiet
a
bout
a
Cy
g
win issue
commit
|
commitdiff
|
tree
2012-03-18
Mark
Abraham
W
a
rn
i
n
gs against equilibrati
n
g with P-R P-coupling
commit
|
commitdiff
|
tree
2012-03-15
Mark Abra
h
am
Clarified wo
r
di
n
g of documentation
commit
|
commitdiff
|
tree
2012-03-14
Mark Abraham
C
hanged cryptic error me
s
sages about disk
q
u
o
t
a
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
More editorial
fixes to tool documentation
commit
|
commitdiff
|
tree
2012-03-09
Ma
r
k Abraham
Editorial
changes to
t
o
ols
d
ocumentation
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraham
Improved warning
n
ote
with DD and perio
d
i
c
molecules
commit
|
commitdiff
|
tree
2012-03-08
Mark Ab
r
aham
Made description
s
tring for g_se
l
ect -sele
c
t clearer
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraham
Improv
e
d cryptic error
m
e
s
sage
commit
|
commitdiff
|
tree
2012-02-24
Mark Abraham
Min
o
r f
o
rmatting fixes to
.
mdp option documentati
o
n
commit
|
commitdiff
|
tree
2012-02-23
Mark Abraham
Fix p
d
b2gmx -
c
m
ap
in corner
c
ases
commit
|
commitdiff
|
tree
2012-02-10
Ma
r
k Abraham
Fi
x
ed g_sha
m
using more tha
n
th
r
ee dimensio
n
s
commit
|
commitdiff
|
tree
2012-02-10
Ma
r
k
A
b
raham
Integer
multiplic
a
tion t
h
a
t
checks for overfl
o
w
commit
|
commitdiff
|
tree
2012-02-01
M
a
rk
Abraham
Fixed trjconv -sub
commit
|
commitdiff
|
tree
2012-02-01
Mark A
b
raham
I
mproved error mess
a
g
e
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
M
ade erro
r
me
s
sage
even
more
explicit
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abra
h
am
Corrected
u
se of ?: in conditional
commit
|
commitdiff
|
tree
2012-01-10
Mark Abraham
Fixed use of i
s
finite and _isfi
n
ite
commit
|
commitdiff
|
tree
2012-01-04
Mark
A
braham
Add
e
d CMake
T
o
o
lchain f
i
le for B
l
ueGen
e
/P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraham
Doc
u
mented
the
f
unction of
g_clust
e
r -cl
-
noav
commit
|
commitdiff
|
tree
2011-12-14
Mark
Ab
r
aham
Re-fix
e
d sta
t
ic linking of maths
librari
e
s under UNI
X
commit
|
commitdiff
|
tree
2011-12-13
Mark
Abra
h
am
Rel
a
xed
some assu
m
ptions
about trajectory times
commit
|
commitdiff
|
tree
2011-11-23
Mark Ab
r
aham
Fix
e
d g_angle -f -or
to c
o
py time
s
from -f to -
o
r
commit
|
commitdiff
|
tree
2011-11-02
M
a
rk
A
b
r
a
h
am
Fix for GB, double, SS
E
2 and
o
pt
i
mi
z
ed kern
e
ls
commit
|
commitdiff
|
tree
2011-11-01
Mark Ab
r
a
ham
Tri
g
ger
c
o
rre
c
t ke
r
nels u
n
der C
y
gwin
commit
|
commitdiff
|
tree
2011-10-27
Mar
k
Abraham
Made
readi
n
g of binary
m
atrices more
robust
commit
|
commitdiff
|
tree
2011-10-19
M
ar
k
A
br
a
h
am
Co
r
recte
d
char
g
e of CH
A
RMM zinc io
n
to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Remov
e
d e
r
roneous use of
M
AS
S
V
on Blu
e
G
ene
commit
|
commitdiff
|
tree
2011-10-06
Mark Abra
h
am
F
i
x
es for GB kernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Abrah
a
m
Added tip
for convertin
g
.
xpm to something use
f
ul
commit
|
commitdiff
|
tree
2011-09-26
Mark
Abraham
Dropped some hin
t
s in
the docume
n
t
ation
commit
|
commitdiff
|
tree
2011-09-26
M
a
rk
Abraham
Remov
e
d CMake warning for recent
O
pe
n
M
P
I versions
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
braham
Fix
t
rjconv -sub
commit
|
commitdiff
|
tree
2011-09-15
Mark
Abraham
Warning ab
o
ut t
r
jconv
-
s
ub n
e
eding many files open
commit
|
commitdiff
|
tree
2011-09-15
Ma
r
k
Abrah
a
m
g_sham -mdata i
s
an input file,
no
t
output file
commit
|
commitdiff
|
tree
2011-09-14
Mark A
b
raham
F
o
rmat
w
arning better
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk Abraham
F
i
x pdb2gm
x
-
debu
g
a
n
d
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mark Ab
r
aham
Fix for CMake f
i
ndin
g
LAPACK
commit
|
commitdiff
|
tree
2011-09-13
Mark Abra
h
am
A
dded ACE
a
nd CT3 to CHA
R
MM27
amino
a
cid
s
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fixed charge groups o
f
CHARMM27 DNA/RNA terminal H
commit
|
commitdiff
|
tree
2011-09-13
M
a
r
k
Abraham
Fixes for C
M
ake finding F
O
R
T
RAN library names on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraham
Fix bug with large ints without
MP
I
_IN_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Made grompp note abou
t
non-zero cha
r
ge
more useful
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k
A
braham
Re-impl
e
me
n
ted genera
t
ing de
f
ault protei
n
ind
e
x group
s
commit
|
commitdiff
|
tree
2011-09-01
Mark Ab
r
a
ham
Adjusted co
n
str
u
c
t
ion of def
a
ult
i
nd
e
x groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Fixed c
o
mment
commit
|
commitdiff
|
tree
2011-08-23
M
a
r
k
Ab
r
aham
Fixed g_disre d
e
refer
e
ncing
c
r
commit
|
commitdiff
|
tree
2011-08-23
M
a
rk Ab
r
aham
Typ
o
fi
x
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
E
xplained termin
a
l residues and
A
MBER in
pdb2gmx -h
commit
|
commitdiff
|
tree
2011-08-16
M
a
rk Abraham
Made free ene
r
gy perturbation work with C
M
AP
commit
|
commitdiff
|
tree
2011-08-03
Mark Ab
r
a
h
am
Fixe
d
o
utput
bu
g
in demux
.
p
l
commit
|
commitdiff
|
tree
2011-07-17
Mark
Ab
r
aham
Str
e
a
mlined small part of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark Abra
h
am
Readin
g
a
.
g96 trajecto
r
y
n
o
w
causes fatal error
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Fix some identifier n
a
ming
i
s
su
e
s in last com
m
it
commit
|
commitdiff
|
tree
2011-07-11
Mark Abra
h
am
Avoided some intege
r
overfl
o
ws
commit
|
commitdiff
|
tree
2011-07-08
Mark Abrah
a
m
Clarified us
e
of OPLS
/
AA
z
witterion ter
m
ini
commit
|
commitdiff
|
tree
2011-07-08
Mark
Abr
a
ham
Fix
e
d
i
m
prope
r
file close
w
ith GB and mdrun -debug
commit
|
commitdiff
|
tree
2011-07-08
Ma
r
k Abraham
Made pdb2gm
x
error messa
g
e l
e
s
s
cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Revert "draft
"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Improved error
m
e
ssage and document
a
tion
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
draft
commit
|
commitdiff
|
tree
2011-06-21
M
a
rk Abraham
Ex
p
anded LINCS
w
arning text
commit
|
commitdiff
|
tree
2011-06-07
Mark A
b
raham
Fixed spell
i
ng o
f
repr
o
duci
b
le
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Added reference to
g_sas
-h
commit
|
commitdiff
|
tree
2011-05-11
Mark
A
b
raham
C
l
ean
e
d up g_sas help text
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Abr
a
ham
Adde
d
hint about calling trjco
n
v more
t
h
a
n onc
e
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
S
paced out
parag
r
aphs in
t
rjconv he
l
p
commit
|
commitdiff
|
tree
2011-05-02
M
a
rk Abr
a
ham
Removed duplicate definiti
o
n
of md_print_warn
i
ng()
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraham
F
ixed desc
r
iptio
n
of
.
m
dp option
t
o "h-bond
s
"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Removed unnecessary #i
n
cludes
commit
|
commitdiff
|
tree
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