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Merge "Some changes for md-vv extracted from 4.6" into release-4-5-patches
2013-04-19
Mark Abr
a
h
a
m
Me
r
g
e
"Some changes for md-vv e
x
tracted
fro
m
4
.
6" into
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraham
Bump share
d
o
b
ject version to 7
commit
|
commitdiff
|
tree
2013-01-17
Mark Abrah
a
m
M
erge "F
i
x trjcon
v
-sub
w
it
h
.
t
rr files
"
int
o
release
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ma
r
k
A
braham
Fix
t
rj
c
onv -s
u
b
with
.
t
rr files
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Added check
for valid wall_atomtype in
.
m
d
p
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Velocity-ver
l
et inte
g
ra
t
ors and v-res
c
a
l
e
ar
e
broken
commit
|
commitdiff
|
tree
2013-01-14
Mark
A
braham
Added fatal
error for constraints + L-BF
G
S minimize
r
commit
|
commitdiff
|
tree
2013-01-13
M
a
r
k Abraham
Updated code checks wi
t
h distance restraints
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraha
m
Fi
x
ing trj
c
onv
-sub
commit
|
commitdiff
|
tree
2013-01-13
Mark Ab
r
aham
Noti
n
g that
a
nd w
h
y gmxdump -s -sys
i
s
broken
commit
|
commitdiff
|
tree
2012-09-24
M
ark Abraham
Fix REMD use
o
f
g
mx_large_int_t f
o
r #s
t
ep
s
variable
commit
|
commitdiff
|
tree
2012-09-10
Mark
Abra
h
am
Co
r
r
e
cted REMD citation
commit
|
commitdiff
|
tree
2012-08-31
M
a
rk Abraham
I
mp
r
oved pdb2
g
m
x
o
utput
commit
|
commitdiff
|
tree
2012-08-28
Mark Abraham
Doc
u
m
ent correct comm_mode op
t
i
o
n
commit
|
commitdiff
|
tree
2012-08-10
Mark A
b
raham
Added TIP4P bac
k
into CHARMM27
commit
|
commitdiff
|
tree
2012-06-19
Mar
k
Abraham
M
e
rge "F
i
xes
#882 -
l
ooping
bug in trxi
o
.
c" in
t
o re
l
e
ase
.
.
.
commit
|
commitdiff
|
tree
2012-06-15
Mark Abraham
Q
u
iet li
n
k
e
r on BlueGe
n
e
commit
|
commitdiff
|
tree
2012-06-15
Mark Abraham
Fix g
_
lie countin
g
l
ast frame
t
wice
commit
|
commitdiff
|
tree
2012-06-06
M
a
rk Abra
h
am
Work around failur
e
of endianness tes
t
i
n
g
on
BlueGene
commit
|
commitdiff
|
tree
2012-06-06
Mark Abraham
Fi
x
endian test functiona
l
ity
commit
|
commitdiff
|
tree
2012-06-04
Mark Ab
r
aha
m
Add
e
d more suggested strategies to
error message
commit
|
commitdiff
|
tree
2012-05-31
Mark Abraham
Made mdr
u
n more verbos
e
about P
M
E
s
plit
commit
|
commitdiff
|
tree
2012-05-26
Mark Abraham
Contin
u
i
ng to fix threading on Cygwin
commit
|
commitdiff
|
tree
2012-04-28
Mark A
b
raham
Merge "Remo
v
e ch
e
cks bas
e
d on Gen
e
ra
t
or" into releas
e
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Mark Abraham
Merg
e
"Fi
x
version info
generation
f
or
a
uto
c
onf
.
"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2012-04-19
Mark A
b
raham
Vario
u
s
improvemen
t
s to shell code
commit
|
commitdiff
|
tree
2012-04-14
Mark
A
br
a
ham
Described default output beha
v
i
ou
r
commit
|
commitdiff
|
tree
2012-04-14
Mark Abraham
C
l
arifi
e
d warning m
e
ssage
commit
|
commitdiff
|
tree
2012-04-14
Mark Abraham
Clarified warning strin
g
commit
|
commitdiff
|
tree
2012-04-10
M
a
rk Abraham
Made g_h
e
lix
sensitive to CHA
R
MM a
t
o
m
n
a
m
i
n
g
commit
|
commitdiff
|
tree
2012-04-10
M
a
rk Abr
a
ham
Permit
thre
a
ds build on
Cygwin
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraham
Do
c
umentation and
e
rro
r
m
e
ssage
enhanc
e
men
t
s
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraham
Lots
o
f manual upd
a
tes
commit
|
commitdiff
|
tree
2012-04-09
Ma
r
k Abra
h
am
Consolidated documentation of
.
mdp res
t
raint options
commit
|
commitdiff
|
tree
2012-04-02
Mark Ab
r
aham
Improved
pdb2gmx error message
commit
|
commitdiff
|
tree
2012-04-02
M
ar
k
Abraham
Keep CMake qu
i
et ab
o
ut
a Cygwin issue
commit
|
commitdiff
|
tree
2012-03-18
Mark Abr
a
ham
Warnings
against equilibrating wi
t
h P-R P
-
cou
p
ling
commit
|
commitdiff
|
tree
2012-03-15
Mark Abraham
C
larified w
o
rding
of documentation
commit
|
commitdiff
|
tree
2012-03-14
Mark A
b
raham
Changed
c
ryptic error me
s
sages
a
bout disk quota
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
More editorial fixes to to
o
l documenta
t
i
on
commit
|
commitdiff
|
tree
2012-03-09
M
a
rk Abraham
Editorial changes to tools doc
u
m
e
ntatio
n
commit
|
commitdiff
|
tree
2012-03-08
Mark Abra
h
am
Improved
wa
r
ning n
o
te with DD and periodic
m
ole
c
u
l
e
s
commit
|
commitdiff
|
tree
2012-03-08
M
ark Abraham
Made descriptio
n
string f
o
r g_select -select c
l
eare
r
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraham
Improved cryptic
e
rror m
e
ssage
commit
|
commitdiff
|
tree
2012-02-24
Mar
k
Abraham
Minor format
t
ing
fixes to
.
mdp op
t
ion documentation
commit
|
commitdiff
|
tree
2012-02-23
Mark Abraham
Fix p
d
b2
g
mx -cma
p
i
n co
r
ner
case
s
commit
|
commitdiff
|
tree
2012-02-10
M
ark
A
b
raham
Fixed g_sham using more than three dimens
i
ons
commit
|
commitdiff
|
tree
2012-02-10
Mark Abraham
Integer multipl
i
cat
i
on that checks for ov
e
rflow
commit
|
commitdiff
|
tree
2012-02-01
Mark
Abr
a
ham
Fixe
d
trjconv -sub
commit
|
commitdiff
|
tree
2012-02-01
Mark Abra
h
am
Fixed error
message to identify the correct fil
e
commit
|
commitdiff
|
tree
2012-02-01
Mark
A
bra
h
am
I
m
proved error message
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Me
r
ge "Corre
c
ted use of ?: in
c
onditional" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark
Abraham
Made error message even more explicit
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraha
m
C
o
r
r
ected use
o
f ?: i
n
con
d
i
tional
commit
|
commitdiff
|
tree
2012-01-10
Mark
A
braham
Fixe
d
us
e
of
i
s
finite and _isfinite
commit
|
commitdiff
|
tree
2012-01-04
Mar
k
Abra
h
am
Add
e
d CMake
Toolchain
f
il
e
f
o
r BlueGe
n
e/P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraham
Doc
u
mented
t
he function of g_cluster -
c
l -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark
A
braham
Re-fixed static link
i
n
g
o
f
mat
h
s lib
r
arie
s
under
UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
Relaxed some
assumptions ab
o
ut t
r
ajec
t
o
ry
times
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Only a
n
a
l
ys
e
angle transitions for dihedr
a
l angles
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Added p
r
ot
e
ct
i
ve p
r
eprocessor directives
commit
|
commitdiff
|
tree
2011-11-23
M
ark Abra
h
am
Fixed g_angle -f -or to copy times from -f to
-
or
commit
|
commitdiff
|
tree
2011-11-02
Mark Abraham
Fix for GB, d
o
uble
,
SSE2 and optimized k
e
rnels
commit
|
commitdiff
|
tree
2011-11-01
Mark Abraham
T
rigger correc
t
kernels u
n
der Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abrah
a
m
Made readin
g
of binary matr
i
ces more robust
commit
|
commitdiff
|
tree
2011-10-19
Mark
A
bra
h
am
Co
r
r
e
ct
e
d charge of CHARMM zinc ion to
+2
commit
|
commitdiff
|
tree
2011-10-06
M
ark Abraham
R
e
moved erroneou
s
use of MASSV on B
l
ueGene
commit
|
commitdiff
|
tree
2011-10-06
M
ark Abraham
Fixes for GB ker
n
e
l
commit
|
commitdiff
|
tree
2011-09-27
M
a
r
k Abraha
m
Added tip fo
r
c
onverting
.
x
p
m
t
o something
u
seful
commit
|
commitdiff
|
tree
2011-09-26
Mark Abr
a
ha
m
Dr
o
pp
e
d some hints in the documentation
commit
|
commitdiff
|
tree
2011-09-26
Mar
k
Abraham
Removed CMake warning for recent OpenMPI versions
commit
|
commitdiff
|
tree
2011-09-15
M
ar
k
Abraham
Fix trjconv
-
s
u
b
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Wa
r
ni
n
g
about trjconv -sub nee
d
i
ng m
a
ny f
i
les open
commit
|
commitdiff
|
tree
2011-09-15
Mark A
b
r
aham
g_sham -mdat
a
is an
i
np
u
t file,
n
ot output fil
e
commit
|
commitdiff
|
tree
2011-09-14
Ma
r
k Abraham
Format warn
i
ng better
commit
|
commitdiff
|
tree
2011-09-13
Mar
k
A
b
r
aham
Fix pdb2gmx
-debug
a
n
d
.
h
db f
i
les
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fix for CMake
f
inding
L
APACK
commit
|
commitdiff
|
tree
2011-09-13
Mark
A
b
raham
Ad
d
e
d
ACE
a
n
d
CT3 to CHARMM
2
7 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
a
r
k
Abraham
Fixed
charge g
r
oups
o
f C
H
ARMM27
D
NA/RNA terminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
F
i
x
es for CMa
k
e
f
inding FO
R
TRAN library
name
s
on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraham
Fix bug w
i
th large ints without MPI_IN_P
L
AC
E
commit
|
commitdiff
|
tree
2011-09-01
Mark
A
b
raham
M
ade grompp note abo
u
t non
-
zero cha
r
ge
more useful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
R
e-implemented generating
d
efault protein index groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abrah
a
m
Adjusted
construction of de
f
a
u
lt index gro
u
ps
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
F
ixed co
m
ment
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Fixed g_
d
isre d
e
r
e
f
erencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
T
ypo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
Explai
n
ed terminal residues and
A
MBER in pdb
2
gmx -h
commit
|
commitdiff
|
tree
2011-08-16
M
ark Abrah
a
m
Made free ener
g
y perturb
a
t
i
on work with CM
A
P
commit
|
commitdiff
|
tree
2011-08-03
Mark Abra
h
am
Fixed output bug in demu
x
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Str
e
amlined small par
t
of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark Ab
r
aham
Re
a
ding
a
.
g96 trajectory now causes
fatal error
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Fix
s
ome iden
t
ifier naming issues
in last
c
ommit
commit
|
commitdiff
|
tree
2011-07-11
Mark A
b
raham
Avoided some i
n
teger overf
l
ows
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
aha
m
Clarified use of OPLS/AA
zwitter
i
on term
i
ni
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk Abrah
a
m
Fi
x
ed imp
r
oper file cl
o
se
w
i
th GB and mdrun -debu
g
commit
|
commitdiff
|
tree
2011-07-08
Mark A
b
raham
Made pdb2gmx e
r
ror message less crypt
i
c
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
Abraham
Revert "draf
t
"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Improved er
r
or message and
d
ocum
e
n
t
ation
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
Abraham
d
raft
commit
|
commitdiff
|
tree
next