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Merge "Some changes for md-vv extracted from 4.6" into release-4-5-patches
2011-06-21
M
a
r
k
Abraham
Expanded LIN
C
S warning t
e
xt
commit
|
commitdiff
|
tree
2011-06-07
Mark
Abraham
Fix
e
d spelling of repr
o
ducible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Added
r
eference to g
_
sas -h
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
C
l
ean
e
d up
g_sas hel
p
text
commit
|
commitdiff
|
tree
2011-05-09
Mark Abrah
a
m
Added
hin
t
a
b
o
ut calling trjconv more t
h
a
n
once
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Abraham
Spaced
o
ut paragraphs in
trjconv hel
p
commit
|
commitdiff
|
tree
2011-05-02
M
a
rk Abraham
Re
m
oved
duplicate defin
i
tio
n
of md_print_w
a
rning(
)
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraha
m
Fixed de
s
criptio
n
of
.
mdp opt
i
on to "h-bond
s
"
commit
|
commitdiff
|
tree
2011-04-14
M
ark
A
braham
Removed
unnecessary
#incl
u
des
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
D
eleted duplicated code
commit
|
commitdiff
|
tree
2011-04-14
Mark Abr
a
ham
Move
d
vari
o
us
s
upport
f
uncti
o
ns for do_md
int
o
mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
ark Abraham
Moved iterated-
c
on
s
t
rain
t
s code into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mar
k
A
b
ra
h
am
Moved heuris
t
ic neigh
b
or-list c
o
de int
o
mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraha
m
Fixed
c
o
de
d
uplica
t
i
on
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
F
ix
e
d header
#
i
f
ndef
t
est
commit
|
commitdiff
|
tree
2011-03-30
M
ar
k
Abraham
R
emoved useless
c
onst qualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark Abra
h
am
Suppr
e
ssed Cygwin C
-
only compiler warni
n
gs
commit
|
commitdiff
|
tree
2011-03-26
Mark A
b
raham
Fixed g_clus
t
er logic error
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
M
ade gmx_rmpbc_t o
b
je
c
t fun
c
tio
n
s not
segfault
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fix
e
d
m
atio
.
c sfree() that
m
ade DvdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added grompp note about av
o
idin
g
zero
-
st
e
p EM
commit
|
commitdiff
|
tree
2011-02-16
Mark A
b
ra
h
am
Clarifie
d
source o
f
g_r
m
sf refer
e
nce frame
commit
|
commitdiff
|
tree
2011-02-13
Mark A
b
r
aham
A
d
ded workaround for F_GB
1
3
duplic
a
te
s
commit
|
commitdiff
|
tree
2011-02-13
Ma
r
k
A
braham
Fixed er
r
oneou
s
floating
-
p
o
int comparison
commit
|
commitdiff
|
tree
2011-02-12
M
ark Abraham
Ad
d
ed note
about
d
oing repea
t
inv
o
cations of genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark
Abraham
Re
m
oved ancien
t
CVS t
a
g lines
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
raham
Used s
o
me spacin
g
to make code rea
d
able
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
U
s
ed symbolic
constant m
o
re con
s
i
ste
n
tly
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraha
m
M
a
d
e
the
"
m
u
l
t
ip
l
e settles" fatal error mor
e
hel
p
ful
commit
|
commitdiff
|
tree
2011-02-02
Mark
A
braham
F
ixed minor
i
ssue
w
ith repl
i
ca
e
x
change
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Added
f
orgo
t
ten file
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraha
m
Turned g_options into a norm
a
l GROMACS tool
commit
|
commitdiff
|
tree
2011-01-28
Ma
r
k Abraha
m
Rename
d
s
r
c/tools/o
p
tions
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mark Abrah
a
m
I
mpr
o
v
e
d grom
p
p
documentation
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved
ge
n
i
o
n -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Ab
r
aham
Relocated some t_matrix do
c
umenta
t
i
on
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Impro
v
e
d
do_dssp -ssdump ou
t
put
commit
|
commitdiff
|
tree
2011-01-25
Ma
r
k
Abraham
Impr
o
ved do_dssp -sc ou
t
put
commit
|
commitdiff
|
tree
2011-01-23
Ma
r
k Abraham
Rem
o
ve g
_
h
i
ghway
f
rom list
o
f p
r
ogr
a
m
s
commit
|
commitdiff
|
tree
2011-01-23
Ma
r
k Abra
h
am
Improved c
o
nversion of documentation to LaTe
X
commit
|
commitdiff
|
tree
2011-01-23
Mark Abr
a
ham
I
m
proved consistency
o
f text styl
e
usage
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Min
o
r wording fi
x
es
commit
|
commitdiff
|
tree
2011-01-23
Mar
k
Abraham
Moved options
.
c
t
o tools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark Abrah
a
m
cmake: added bac
k
gsl support (G
M
X_GSL, di
s
abl
e
d by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
M
ark Abrah
a
m
Add
e
d NHE
t
o OPLS
/
AA pdb2
g
mx
hydrogen d
a
taba
s
e
commit
|
commitdiff
|
tree
2011-01-20
Mark Abraham
Mad
e
gmxdump
error message clearer
.
commit
|
commitdiff
|
tree
2011-01-18
Mark A
b
raham
I
m
proved
.
m
d
p
file comment
a
b
out the 'defi
n
e' f
i
eld
commit
|
commitdiff
|
tree
2011-01-17
Mar
k
Abraham
Fix
Angstrom <=
>
n
m
e
r
ror in documen
t
ation
commit
|
commitdiff
|
tree
2011-01-13
Mark A
b
rah
a
m
Made src/kernel/repl_ex
.
c
legible
commit
|
commitdiff
|
tree
2011-01-07
Mark Abraham
Added note tha
t
g
_
msd -mol doe
s
tr
e
at
PBC (by
m
aki
n
g
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Mark Abrah
a
m
Implemented eff
e
c
t
i
ve test for MPI_IN_P
L
ACE, thanks
.
.
.
commit
|
commitdiff
|
tree
2011-01-06
Mark
Abrah
a
m
Stop C
M
ake defau
l
ting
to t
u
rning off
comp
i
ler warnings
.
.
.
commit
|
commitdiff
|
tree
2010-12-06
Mark A
b
raha
m
Added comments and workaround fo
r
IBM's BlueG
e
ne
(
/L
.
.
.
commit
|
commitdiff
|
tree
2010-11-22
Mark Ab
r
a
h
am
Ad
d
ed a hint t
o
the docume
n
tation for cr
e
a
t
ing
.
tpr
.
.
.
commit
|
commitdiff
|
tree
2010-11-12
Mark Abraham
Mi
n
or tr
j
c
o
nv
docume
n
tation formatting fi
x
commit
|
commitdiff
|
tree
2010-11-12
Mark A
b
raham
g
_
de
n
smap
-
od w
r
ites a
.
dat file and prevents writi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Mark Abraham
GMX_POWER
P
C_INVSQRT should be OFF in
C
Mak
e
Lis
t
s
.
txt
.
.
.
commit
|
commitdiff
|
tree
2010-11-07
Mark Abr
a
ham
Mad
e
mdr
u
n e
x
it with a fata
l
error
f
o
r EM or NM with
.
.
.
commit
|
commitdiff
|
tree
2010-11-06
Mark
A
braham
Fixed
.
xvg le
g
ends f
o
r g_sas options -or a
n
d -
o
a
commit
|
commitdiff
|
tree
2010-10-24
Mark Abraham
D
o
n
'
t s
p
rin
t
f
variable-s
i
zed input into fi
x
e
d-size
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mar
k
Abraham
Re-en
a
bled for Blu
e
G
e
ne/L an optimization
in the BG
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
M
ark Abraham
Rearranged
cmak
e
+BlueGe
n
e solu
t
i
on to have the same
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark A
b
raham
Made GMX_POWERPC_
I
NVSQRT work properly on Power6 and
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Ma
r
k A
b
raha
m
P
o
wer6 FOR
T
RAN kernel
s
d
o not work on
PPC440 o
r
PPC450
.
.
.
commit
|
commitdiff
|
tree
2010-10-22
Mark Abraha
m
F
i
xing
a trivial m
a
n
gle introduced in
b
5
d842ff1
d
94174b6e7012
.
.
.
commit
|
commitdiff
|
tree
2010-10-20
Mark A
b
rah
a
m
Fixe
d
cma
k
e to work with BlueGene/
L
.
This fix does
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Mark Abraham
Fix m
a
nual refere
n
ces for
'co
n
tinua
t
ion',
r
athe
r
than
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
M
ark
Abr
a
h
am
mk_dlist(
)
changed
it
s
par
a
meter list, so its dec
l
ara
t
ion
.
.
.
commit
|
commitdiff
|
tree
2010-09-23
Mark Abraham
Fixes for g_chi
f
or bugzilla 569, so tha
t
it now uses
.
.
.
commit
|
commitdiff
|
tree
2010-09-23
Mar
k
Abraham
E
x
tensions to the gmx
_
residuetypes_t
API to meet the
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Mark Abraham
When grompp failed to find t
h
e forcefield, the error
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Mark Ab
r
aham
Formatting
f
ixes t
o
documentat
i
on
commit
|
commitdiff
|
tree
2010-09-09
M
ark A
b
r
a
h
am
A
d
d
ed T
I
P5p to CHARMM forcef
i
e
ld b
y
analogy with AMBER03
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Mark A
b
rah
a
m
Spelling fix
commit
|
commitdiff
|
tree
2010-09-08
Mar
k
Ab
r
aham
Added note to
g
_covar abo
u
t memory costs
a
nd managing
.
.
.
commit
|
commitdiff
|
tree
2010-09-02
Mark Abraham
Fix s
p
elling error
commit
|
commitdiff
|
tree
2010-09-01
Mar
k
A
b
raham
Formatting
f
ixes
to document
a
tion
commit
|
commitdiff
|
tree
2010-09-01
M
ark
Abraham
Merge branch '
r
elease-4-5-p
a
tches' of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
M
ark Abraham
make_opt
.
html now doesn't use
<
h4>, rather
i
t
u
ses
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
M
ark Abraham
General
f
ixes
commit
|
commitdiff
|
tree
2010-08-30
M
ar
k
A
b
r
aham
Mad
e
a pdb2gmx
m
essage
l
ess cryptic
w
h
e
n it finds mu
l
tiple
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Mark
A
br
a
ha
m
Spelling fi
x
e
s
in pdb2gmx documen
t
ation
commit
|
commitdiff
|
tree
2010-08-26
Ma
r
k Ab
r
a
h
am
M
a
de
the descri
p
tion
o
f ld_see
d
and gen_seed seed ge
n
e
ration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Mark A
b
raha
m
F
i
xe
d
HT
M
L documentation to use pr
o
per '
&
g
e',
n
ot
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Ma
r
k
Abraham
C
l
a
rified documentation abo
u
t
when
gen_v
e
l
generates
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Mar
k
Abrah
a
m
Fixed
l
eak fr
o
m un
c
los
e
d directory h
a
nd
l
es when pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Mark Abraham
Made
pdb2g
m
x be slightly more hel
p
fu
l
when using AMBER
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
M
a
rk
A
braha
m
Two spelli
n
g fixes in c
o
m
m
ent a
n
d output
commit
|
commitdiff
|
tree
2010-06-24
Ma
r
k Abra
h
am
Added snew_alig
n
ed and sfree_al
i
gn
e
d for mana
g
ing n
.
.
.
commit
|
commitdiff
|
tree