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4.5.7 release
2013-04-19
Mark Abra
h
am
4
.
5
.
7 relea
s
e
commit
|
commitdiff
|
tree
2013-04-19
M
i
chael Sh
i
rts
So
m
e
changes f
o
r
md
-
vv e
x
tracted from 4
.
6
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Bump shared ob
j
ect
ver
s
ion t
o
7
commit
|
commitdiff
|
tree
2013-01-15
Mark Abr
a
ham
Add
e
d
c
h
e
c
k for valid
wall_
a
tomty
p
e in
.
mdp
commit
|
commitdiff
|
tree
2013-01-14
M
a
rk Abr
a
ham
Added f
a
ta
l
error
f
o
r
c
onst
r
aints
+
L-BFGS
m
inimize
r
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Upda
t
ed c
o
d
e checks wi
t
h
d
istance
r
estraints
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Fixing tr
j
conv -s
u
b
commit
|
commitdiff
|
tree
2013-01-13
M
a
rk Abraham
No
t
ing
t
hat a
n
d why gmxdump -s -sys is
broke
n
commit
|
commitdiff
|
tree
2012-09-24
Mark Abraham
Fix
REMD use of gmx_large_int_t for #steps variable
commit
|
commitdiff
|
tree
2012-09-10
Mark
A
braha
m
Correc
t
ed REMD ci
t
ation
commit
|
commitdiff
|
tree
2012-08-31
Mar
k
Abr
a
ham
I
m
prov
e
d pdb2g
m
x output
commit
|
commitdiff
|
tree
2012-08-28
Mark
A
braham
Document correct comm_mode
o
pti
o
n
commit
|
commitdiff
|
tree
2012-08-10
Mark Abr
a
ham
Add
e
d TIP4P
b
a
c
k int
o
C
H
ARMM27
commit
|
commitdiff
|
tree
2012-06-15
Mark Abr
a
ham
Quiet linker
o
n BlueGen
e
commit
|
commitdiff
|
tree
2012-06-15
Mark Abraham
Fix
g_lie counting last f
r
am
e
tw
i
ce
commit
|
commitdiff
|
tree
2012-06-06
Mark Abraham
Wor
k
a
round fail
u
re
o
f
e
ndianness testing on BlueGen
e
commit
|
commitdiff
|
tree
2012-06-06
Mar
k
Abraham
Fix en
d
ian test functionality
commit
|
commitdiff
|
tree
2012-06-04
Mark
A
bra
h
am
Added
mor
e
s
u
ggested stra
t
egies t
o
e
r
ror mess
a
ge
commit
|
commitdiff
|
tree
2012-05-31
Ma
r
k Abraham
Mad
e
md
r
un more
verbose about PME
split
commit
|
commitdiff
|
tree
2012-05-26
M
ark Ab
r
aha
m
Continu
i
ng t
o
fix th
r
eading on Cygw
i
n
commit
|
commitdiff
|
tree
2012-04-19
M
a
rk Abra
h
am
V
a
r
i
ous impro
v
em
e
nts to shell code
commit
|
commitdiff
|
tree
2012-04-14
Mark Abraham
Described
def
a
ult output behaviour
commit
|
commitdiff
|
tree
2012-04-14
Mark Abraham
Clar
i
f
i
ed warnin
g
message
commit
|
commitdiff
|
tree
2012-04-14
Mark
A
braham
Clarified warning string
commit
|
commitdiff
|
tree
2012-04-10
Mark Abr
a
ha
m
M
ade g_helix sensit
i
v
e
t
o
CHARMM atom na
m
ing
commit
|
commitdiff
|
tree
2012-04-10
Mark Abraha
m
Permit threads build on
C
y
gwin
commit
|
commitdiff
|
tree
2012-04-09
M
a
rk
Abrah
a
m
Documentatio
n
a
nd error
m
essage
e
nhancements
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraham
Lots of manual upd
a
tes
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraha
m
C
o
nsolidate
d
documentation o
f
.
mdp
restraint options
commit
|
commitdiff
|
tree
2012-04-02
Mark
A
bra
h
am
Impro
v
ed pdb2gmx
e
rror message
commit
|
commitdiff
|
tree
2012-04-02
Ma
r
k
A
br
a
h
a
m
K
eep
CMake quiet abou
t
a C
y
g
w
in issue
commit
|
commitdiff
|
tree
2012-03-18
Mark Abraha
m
W
a
rni
n
gs a
g
a
inst equilibrati
n
g with P-R P-c
o
u
p
ling
commit
|
commitdiff
|
tree
2012-03-15
Mark Abraham
Cla
r
ified wording of documentation
commit
|
commitdiff
|
tree
2012-03-14
M
a
rk Abraham
Change
d
cryptic error mes
s
ages about disk
q
uot
a
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
More e
d
ito
r
i
a
l fixes to tool do
c
umentation
commit
|
commitdiff
|
tree
2012-03-09
M
ark A
b
raham
Editorial changes to tools documentat
i
on
commit
|
commitdiff
|
tree
2012-03-08
M
a
rk Abraham
Impr
o
ved warning note w
i
t
h
D
D and pe
r
iodic
m
ole
c
ul
e
s
commit
|
commitdiff
|
tree
2012-03-08
M
a
r
k
Abraham
M
a
de descri
p
tion s
t
ring
f
or g_
s
e
l
ect -s
e
lect clearer
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraham
Improved cryptic error
message
commit
|
commitdiff
|
tree
2012-02-24
Ma
r
k
Abraham
Min
o
r formatti
n
g f
i
xes to
.
md
p
option documentati
o
n
commit
|
commitdiff
|
tree
2012-02-23
M
ark
A
braham
Fix pdb2gmx -cmap in corner
c
a
s
e
s
commit
|
commitdiff
|
tree
2012-02-10
M
a
rk Abraha
m
Fixed g_sh
a
m using more than
three dimens
i
o
n
s
commit
|
commitdiff
|
tree
2012-02-10
Mark Abra
h
am
Integer multi
p
lica
t
i
on that checks for overflow
commit
|
commitdiff
|
tree
2012-02-01
Ma
r
k Abraham
Fi
x
ed trjc
o
nv -sub
commit
|
commitdiff
|
tree
2012-02-01
Ma
r
k Abraham
I
mproved error messag
e
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abraham
M
a
de err
o
r
m
essage even
more explicit
commit
|
commitdiff
|
tree
2012-01-31
Mark Ab
r
aham
C
orrected us
e
of
?:
in conditional
commit
|
commitdiff
|
tree
2012-01-10
Mark Abraham
Fi
x
e
d
u
se of isfinit
e
and _isfinite
commit
|
commitdiff
|
tree
2012-01-04
M
ark Abraham
Added
CMake Toolchain file for BlueGene/P
commit
|
commitdiff
|
tree
2011-12-29
M
ark Abraham
Docu
m
ented the functi
o
n of g_cluster -cl -noav
commit
|
commitdiff
|
tree
2011-12-14
M
a
rk Abraham
R
e
-fi
x
ed s
t
atic linking of maths l
i
bra
r
ies under
U
NIX
commit
|
commitdiff
|
tree
2011-12-13
Mark
A
braham
R
ela
x
ed
some assumpti
o
n
s about
t
rajectory ti
m
es
commit
|
commitdiff
|
tree
2011-11-23
Mark Abraham
Fixed g_an
g
le
-
f
-or to
c
opy tim
e
s from -
f
to
-or
commit
|
commitdiff
|
tree
2011-11-02
Mark Ab
r
aha
m
Fix for GB, double, SSE2 and optimized ker
n
els
commit
|
commitdiff
|
tree
2011-11-01
M
ark
A
braham
Tr
i
g
ger correct ke
r
nels u
n
der Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abraham
M
a
de read
i
n
g
of binary
m
a
trices
m
ore r
o
b
u
st
commit
|
commitdiff
|
tree
2011-10-19
M
a
rk Abra
h
am
C
o
rrected char
g
e
of CHARMM zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
M
a
rk Abraha
m
Removed erroneous
use o
f
MAS
S
V on BlueGene
commit
|
commitdiff
|
tree
2011-10-06
M
a
r
k Abraham
Fixes for GB
k
ernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraham
Added tip
f
or convertin
g
.
xpm to something use
f
ul
commit
|
commitdiff
|
tree
2011-09-26
Mar
k
Abraham
Dropped
s
ome h
i
nts
i
n
t
h
e do
c
umentation
commit
|
commitdiff
|
tree
2011-09-26
M
a
rk Abraham
Removed CMake warning for rec
e
n
t
OpenM
P
I version
s
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Fix trjc
o
nv -sub
commit
|
commitdiff
|
tree
2011-09-15
Mark
Abraham
Warning about trjconv -sub needing many files open
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
g
_
s
ham -
m
data
is an input
file, not
o
utput file
commit
|
commitdiff
|
tree
2011-09-14
M
a
rk
A
braham
F
ormat warning
better
commit
|
commitdiff
|
tree
2011-09-13
Mark Abrah
a
m
F
i
x pdb2gmx -deb
u
g and
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
F
i
x for CMake finding LA
P
ACK
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
r
aham
Ad
d
e
d ACE and CT3 to CHAR
M
M27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk A
b
r
a
ha
m
Fixed charge groups of CH
A
RM
M
27
D
NA
/
RNA
t
erminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark
Abraham
Fixes for CMake finding FORTRAN library names on POWE
R
6
commit
|
commitdiff
|
tree
2011-09-06
Mark
A
braham
F
i
x bug with
l
arge
i
nts with
o
ut MPI_IN_PLA
C
E
commit
|
commitdiff
|
tree
2011-09-01
Mar
k
A
b
raham
M
a
de grompp note ab
o
u
t n
o
n-zero charge mo
r
e useful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
R
e-impl
e
mented generating default protein
i
ndex group
s
commit
|
commitdiff
|
tree
2011-09-01
Mark Ab
r
ah
a
m
A
djusted
constructi
o
n
o
f d
e
fault index group
s
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mar
k
Abr
a
ham
F
i
xed g_disre derefe
r
enci
n
g
c
r
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
Explained terminal residues
and AMBER in pd
b
2
g
m
x
-
h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abraham
Made free energy perturbation work
wi
t
h CMAP
commit
|
commitdiff
|
tree
2011-08-03
M
ark
Abraham
Fixed output bu
g
in demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Streamlined small part of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
M
a
rk Abraham
Reading a
.
g
96 trajector
y
now
causes fata
l
error
commit
|
commitdiff
|
tree
2011-07-11
Mark Ab
r
a
ham
F
i
x
some ide
n
tifie
r
na
m
ing
i
ssues in last comm
i
t
commit
|
commitdiff
|
tree
2011-07-11
Mark
Abraham
A
void
e
d
som
e
integer overflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
a
ham
Clar
i
fied use
o
f
O
PLS/AA zwi
t
t
erion termini
commit
|
commitdiff
|
tree
2011-07-08
Mar
k
Abraham
Fix
e
d improper file close wi
t
h GB and mdrun
-
deb
u
g
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk Abraham
Made pdb2gmx error message
less cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
A
braham
Rever
t
"d
r
aft"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Impro
v
ed erro
r
me
s
sage and
d
o
c
umentatio
n
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
Abraham
draft
commit
|
commitdiff
|
tree
2011-06-21
Mark Abraham
Expanded
L
I
NC
S
warn
i
ng tex
t
commit
|
commitdiff
|
tree
2011-06-07
Mark Abraham
Fixed spelling of
reprod
u
cible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Added referen
c
e to g_sas
-
h
commit
|
commitdiff
|
tree
2011-05-11
Ma
r
k Abrah
a
m
C
l
e
an
e
d
up g_sas help
t
ext
commit
|
commitdiff
|
tree
2011-05-09
Mar
k
Ab
r
a
ham
A
d
ded
h
int a
b
out calling trjconv
m
o
r
e than on
c
e
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
S
paced
out paragraphs
i
n trjcon
v
help
commit
|
commitdiff
|
tree
2011-05-02
Mark
A
b
r
aham
Rem
o
ved
du
p
licate
d
efiniti
o
n of m
d
_print_warning(
)
commit
|
commitdiff
|
tree
2011-05-01
Mar
k
Abraham
F
i
xed descr
i
ption of
.
mdp option to
"h-bonds"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Removed unnecessary #includes
commit
|
commitdiff
|
tree
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