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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
ham
Mer
g
e "Some changes f
o
r
md-vv extr
a
cte
d
from
4
.
6"
i
nt
o
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mark Abra
h
am
B
u
mp shared ob
j
ect version to 7
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Mer
g
e
"
F
ix
trjcon
v
-sub w
i
th
.
trr files" into r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
braham
Fix t
r
jconv -sub
w
it
h
.
trr files
commit
|
commitdiff
|
tree
2013-01-15
Ma
r
k Abraham
Added
chec
k
fo
r
valid
wall_atomtype
i
n
.
mdp
commit
|
commitdiff
|
tree
2013-01-15
Ma
r
k A
b
raham
V
e
l
ocity-verlet
in
t
egrato
r
s
and v-rescale are
broken
commit
|
commitdiff
|
tree
2013-01-14
Mark
Abraham
A
d
ded f
a
tal er
r
or
for constraint
s
+ L-BFGS minimize
r
commit
|
commitdiff
|
tree
2013-01-13
Mark Abra
h
am
Updated code checks with distan
c
e restraints
commit
|
commitdiff
|
tree
2013-01-13
Mar
k
Ab
r
aham
Fi
x
ing trjcon
v
-su
b
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
No
t
i
n
g that and why g
m
xdump -s -sys is bro
k
en
commit
|
commitdiff
|
tree
2012-09-24
M
ark
A
braham
Fix
RE
M
D use of gm
x
_lar
g
e_int_t for #steps
v
ariable
commit
|
commitdiff
|
tree
2012-09-10
M
a
rk Abraham
Corrected REMD citat
i
on
commit
|
commitdiff
|
tree
2012-08-31
Ma
r
k Abraham
Improved pdb2
g
mx output
commit
|
commitdiff
|
tree
2012-08-28
Mark Abraham
Doc
u
ment correc
t
comm_m
o
d
e
opti
o
n
commit
|
commitdiff
|
tree
2012-08-10
Mark Abraha
m
Added TIP4P back into CHARMM27
commit
|
commitdiff
|
tree
2012-06-19
Mark Abra
h
a
m
Me
r
g
e
"Fix
e
s #
8
82 - loopin
g
bug in
trxio
.
c" i
n
to release
.
.
.
commit
|
commitdiff
|
tree
2012-06-15
Mark
A
b
raham
Quiet
l
i
n
ker on BlueG
e
ne
commit
|
commitdiff
|
tree
2012-06-15
Mark
A
braham
Fix g_lie cou
n
t
i
ng l
a
st frame twice
commit
|
commitdiff
|
tree
2012-06-06
Mark Abraham
W
ork around
fail
u
re of endi
a
n
ness testing on
B
l
ueGe
n
e
commit
|
commitdiff
|
tree
2012-06-06
M
a
rk Abraham
Fix
en
d
ian test functionality
commit
|
commitdiff
|
tree
2012-06-04
Mark A
b
raham
Added more
s
uggested strate
g
ies to
e
rror mess
a
ge
commit
|
commitdiff
|
tree
2012-05-31
Mark Abraham
Made mdrun more verbos
e
about PME split
commit
|
commitdiff
|
tree
2012-05-26
Mar
k
Abraham
Continuin
g
t
o
fix
thre
a
d
i
ng on Cygwin
commit
|
commitdiff
|
tree
2012-04-28
M
a
rk A
b
raham
Merge
"
Remove
c
hecks based
on Generat
o
r"
i
nto release
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Mark Abraham
Merge "Fix v
e
r
si
o
n inf
o
g
eneration for
autoconf
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-04-19
Mark Abrah
a
m
Vario
u
s improvem
e
n
t
s
to
s
hell c
o
de
commit
|
commitdiff
|
tree
2012-04-14
Mark Ab
r
aham
D
escrib
e
d default
output
b
ehaviour
commit
|
commitdiff
|
tree
2012-04-14
M
ark Abraham
Clarified war
n
ing
m
essage
commit
|
commitdiff
|
tree
2012-04-14
Mark A
b
ra
h
a
m
Clarified warnin
g
string
commit
|
commitdiff
|
tree
2012-04-10
Mark
Abraha
m
M
a
de g_helix sen
s
i
tive to C
H
ARMM atom naming
commit
|
commitdiff
|
tree
2012-04-10
Mark Abraham
Pe
r
m
i
t thread
s
build on Cygw
i
n
commit
|
commitdiff
|
tree
2012-04-09
Mark Abr
a
ha
m
D
o
c
umentation
and erro
r
m
e
ssage
e
nha
n
cements
commit
|
commitdiff
|
tree
2012-04-09
Mark
A
b
r
a
ham
L
o
ts of manual up
d
a
t
es
commit
|
commitdiff
|
tree
2012-04-09
Mark Abraham
Co
n
soli
d
a
t
ed docume
n
tation o
f
.
mdp rest
r
aint option
s
commit
|
commitdiff
|
tree
2012-04-02
Ma
r
k
A
braham
Imp
r
oved p
d
b
2
gmx er
r
or message
commit
|
commitdiff
|
tree
2012-04-02
Mark Abraham
Keep CMake
q
u
iet
a
bou
t
a Cygwin issue
commit
|
commitdiff
|
tree
2012-03-18
Mark A
b
rah
a
m
Warnings aga
i
nst equilib
r
ating
w
ith P-R P-cou
p
ling
commit
|
commitdiff
|
tree
2012-03-15
Mark Abraham
Clarified wo
r
ding of docum
e
n
tation
commit
|
commitdiff
|
tree
2012-03-14
Mark Abra
h
a
m
Changed
c
ryptic error messages about disk
q
u
o
t
a
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
Mor
e
editorial fi
x
es to tool documentation
commit
|
commitdiff
|
tree
2012-03-09
Mark Abraham
E
ditorial c
h
ange
s
to tool
s
d
o
cument
a
t
i
on
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraha
m
Improved warning note with DD and periodic
molecules
commit
|
commitdiff
|
tree
2012-03-08
Mark Abraha
m
M
a
de
d
e
s
c
r
i
p
tion string
for
g_select -s
e
lect clea
r
er
commit
|
commitdiff
|
tree
2012-03-08
Mark Ab
r
aham
Improved
c
ryptic error message
commit
|
commitdiff
|
tree
2012-02-24
Ma
r
k A
b
raham
Min
o
r
formatting
f
ixe
s
to
.
mdp option document
a
t
i
on
commit
|
commitdiff
|
tree
2012-02-23
Ma
r
k Abraham
Fix
p
d
b2gm
x
-cmap in
c
o
rner cases
commit
|
commitdiff
|
tree
2012-02-10
Mark Abraham
Fixed g_sham using more than three dimension
s
commit
|
commitdiff
|
tree
2012-02-10
Mar
k
Abraham
Intege
r
multiplication that checks
for o
v
erflow
commit
|
commitdiff
|
tree
2012-02-01
Mark Abraham
Fixed t
r
jconv -sub
commit
|
commitdiff
|
tree
2012-02-01
Mark Abrah
a
m
F
i
xed error
messa
g
e to identify the correct file
commit
|
commitdiff
|
tree
2012-02-01
Mar
k
Abraham
Impr
o
ved error
m
essage
commit
|
commitdiff
|
tree
2012-01-31
Mark Abr
a
ham
Merge "Corr
e
ct
e
d use of ?: in c
o
n
dit
i
onal" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Made er
r
o
r
m
e
s
sage
e
v
en more explici
t
commit
|
commitdiff
|
tree
2012-01-31
M
a
r
k
Abr
a
ham
Correc
t
e
d use of ?:
in conditional
commit
|
commitdiff
|
tree
2012-01-10
Mark Ab
r
aham
Fix
e
d use of isfi
n
ite and
_isfi
n
ite
commit
|
commitdiff
|
tree
2012-01-04
Mark Abraham
Added CMak
e
Tool
c
h
a
in fil
e
for BlueGene/
P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraham
Documented the function of g_clus
t
er -cl -n
o
a
v
commit
|
commitdiff
|
tree
2011-12-14
Mark A
b
raham
Re-fixed s
t
a
t
ic linking
o
f math
s
librar
i
es
under UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abrah
a
m
Relaxed so
m
e assumptions about
traje
c
to
r
y
t
i
me
s
commit
|
commitdiff
|
tree
2011-11-24
Mark Abra
h
am
Only analyse angle transit
i
o
n
s for dihedral angles
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Added protective
preprocessor direc
t
ives
commit
|
commitdiff
|
tree
2011-11-23
Mark Abraham
Fixed g_angle -f -or to co
p
y times from
-f to -or
commit
|
commitdiff
|
tree
2011-11-02
M
ark A
b
raham
Fix for
G
B, double, SSE2
an
d
optimiz
e
d k
e
rnel
s
commit
|
commitdiff
|
tree
2011-11-01
Mark Abrah
a
m
Trigg
e
r correct k
e
rnels under Cygwin
commit
|
commitdiff
|
tree
2011-10-27
M
ark Abra
h
a
m
M
ade reading of binary matrices more robust
commit
|
commitdiff
|
tree
2011-10-19
Mark Ab
r
aham
Corrected charge of CHARMM zinc i
o
n
to
+2
commit
|
commitdiff
|
tree
2011-10-06
M
ark Abraha
m
Removed erroneous us
e
of
M
ASSV on BlueGen
e
commit
|
commitdiff
|
tree
2011-10-06
Ma
r
k Abr
a
ham
Fixes
f
or
G
B ke
r
nel
commit
|
commitdiff
|
tree
2011-09-27
M
a
rk Abra
h
am
Added
t
ip for convertin
g
.
x
p
m
t
o s
o
me
t
h
ing
us
e
f
u
l
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dr
o
p
ped s
o
me hints in
the docum
e
ntation
commit
|
commitdiff
|
tree
2011-09-26
Mark Ab
r
aham
R
emoved
CM
a
ke
w
a
r
n
ing for recent OpenMPI
v
e
r
sions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abra
h
am
Fix
trjconv
-
s
u
b
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
b
r
aham
Warni
n
g about trj
c
onv -sub needing m
a
ny files open
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
braham
g_sham -m
d
ata
is an
i
n
p
ut file, not output file
commit
|
commitdiff
|
tree
2011-09-14
M
a
rk
A
braham
Format warni
n
g
bett
e
r
commit
|
commitdiff
|
tree
2011-09-13
M
a
r
k
Abra
h
am
F
ix p
d
b
2gmx
-
d
eb
u
g
an
d
.
hdb fil
e
s
commit
|
commitdiff
|
tree
2011-09-13
Mark
Abraham
F
ix for CMake find
i
ng
LAPACK
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
raham
Added ACE and
C
T
3
to CH
A
RMM2
7
a
minoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk Abra
h
am
Fixed cha
r
g
e
gro
u
ps of
C
HARMM27
DNA/R
N
A t
e
rminal H
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abra
h
am
F
i
x
e
s for CMake find
i
ng FORTRAN librar
y
na
m
es on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraham
Fi
x
bug with
large ints wit
h
out M
P
I_
I
N_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Mark
A
braham
Made grompp note ab
o
u
t non-
z
ero charge more u
s
eful
commit
|
commitdiff
|
tree
2011-09-01
Mark
A
b
raham
Re-i
m
plemente
d
gener
a
ting
default
protein i
n
d
e
x
g
r
oups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abr
a
ha
m
A
djusted constructi
o
n of d
e
fa
u
lt index groups
commit
|
commitdiff
|
tree
2011-09-01
Mar
k
Ab
r
aham
Fixed com
m
ent
commit
|
commitdiff
|
tree
2011-08-23
Mark A
b
raham
Fixed g_dis
r
e
dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Ma
r
k
A
braham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abra
h
am
E
xplained terminal re
s
idues and AMBER i
n
pd
b
2gmx
-h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abraham
Mad
e
free
e
n
e
r
g
y
per
t
u
rbation work with CMAP
commit
|
commitdiff
|
tree
2011-08-03
Ma
r
k Abraham
Fixe
d
output bug
in demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Ma
r
k
A
bra
h
a
m
Str
e
a
mlined small part
of pdb2gm
x
commit
|
commitdiff
|
tree
2011-07-15
Mark Abraham
Reading a
.
g96 t
r
ajector
y
now
c
a
uses fatal erro
r
commit
|
commitdiff
|
tree
2011-07-11
Mark A
b
raham
Fix some
identifier naming issues
i
n last commit
commit
|
commitdiff
|
tree
2011-07-11
Ma
r
k Abraha
m
Avoided some
intege
r
o
v
e
rflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Clarified use of OPLS/AA zwitterion te
r
mini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Fixed im
p
roper file
c
lose
with GB and md
r
un -
d
e
b
ug
commit
|
commitdiff
|
tree
2011-07-08
Ma
r
k Abraham
Made pdb2
g
mx error message less cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Rev
e
rt "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
Impr
o
ved e
r
ror mess
a
ge and docu
m
entatio
n
commit
|
commitdiff
|
tree
2011-06-29
Mark Abr
a
ham
d
raft
commit
|
commitdiff
|
tree
next