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Fixed trjconv -sub
2012-02-01
Mark Abraham
Fixed trj
c
onv
-sub
commit
|
commitdiff
|
tree
2012-01-31
M
a
r
k
Ab
r
a
h
a
m
Merg
e
"
Corrected use
of ?:
in
c
o
nditional"
i
n
to release
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark
A
braham
Made error messag
e
even more explici
t
commit
|
commitdiff
|
tree
2012-01-31
M
a
r
k Abr
a
ham
Corrected use of ?: in conditi
o
na
l
commit
|
commitdiff
|
tree
2012-01-10
Mark Abraham
F
ixed
u
se of i
s
finite a
n
d
_isfinite
commit
|
commitdiff
|
tree
2012-01-04
Mark Abraham
A
d
de
d
C
M
a
ke Toolchain file for BlueGe
n
e/P
commit
|
commitdiff
|
tree
2011-12-29
M
a
r
k
Abraham
D
o
c
umented th
e
functio
n
of g_cluster
-
cl -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark Abra
h
am
R
e-fixe
d
static linking of
m
at
h
s librar
i
es under UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abr
a
ham
Relaxed so
m
e assumptions about traje
c
tory tim
e
s
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Only an
a
lyse angle tr
a
ns
i
tion
s
for dihedral angles
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Added protective prepro
c
esso
r
direc
t
ives
commit
|
commitdiff
|
tree
2011-11-23
Mark
A
b
raham
Fixed g_ang
l
e -f -or to copy time
s
f
ro
m
-f to -or
commit
|
commitdiff
|
tree
2011-11-02
Mark
A
braham
F
ix for GB, double,
SSE
2
and op
t
i
miz
e
d ke
r
n
els
commit
|
commitdiff
|
tree
2011-11-01
Mark Abraham
Trig
g
er cor
r
ec
t
k
ern
e
ls unde
r
Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abraham
Made reading
o
f binary matrice
s
more robus
t
commit
|
commitdiff
|
tree
2011-10-19
Mark Abr
a
ha
m
Corrected cha
r
ge of CHARMM zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
Ma
r
k Ab
r
aham
Removed erroneous use
of MASSV on BlueGene
commit
|
commitdiff
|
tree
2011-10-06
Mark
A
braham
F
i
x
e
s for GB kernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraha
m
Adde
d
tip for converting
.
xpm to s
o
meth
i
ng usefu
l
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dropped
some hints in the do
c
umentation
commit
|
commitdiff
|
tree
2011-09-26
Ma
r
k Abra
h
am
Rem
o
ve
d
CMa
k
e warning for recent O
p
enMPI vers
i
ons
commit
|
commitdiff
|
tree
2011-09-15
M
a
rk Abraham
Fix
trjconv -
s
u
b
commit
|
commitdiff
|
tree
2011-09-15
M
a
rk Abraham
Warni
n
g ab
o
u
t
trjconv -sub needing m
a
ny
files open
commit
|
commitdiff
|
tree
2011-09-15
Mark
Abraham
g
_
sham -mdata is a
n
input
f
ile, no
t
outpu
t
f
i
l
e
commit
|
commitdiff
|
tree
2011-09-14
Mark Abraham
Forma
t
w
arning better
commit
|
commitdiff
|
tree
2011-09-13
Mark
Ab
r
aham
Fix pdb2gm
x
-
d
e
b
ug and
.
h
d
b files
commit
|
commitdiff
|
tree
2011-09-13
Mar
k
Abr
a
ham
F
i
x
f
o
r
C
M
a
k
e finding
LAPACK
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraha
m
Added ACE a
n
d CT3 to
CHARMM27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fixed charge
groups
o
f CHARMM27 D
N
A
/RNA termina
l
H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraha
m
F
i
xes
f
o
r CMake finding FORTRA
N
lib
r
ary names on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraha
m
Fix b
u
g with la
r
ge int
s
without
M
P
I_IN_PLA
C
E
commit
|
commitdiff
|
tree
2011-09-01
Mark
A
braha
m
Made grompp note
a
bout
n
on-ze
r
o c
h
arge
mor
e
usef
u
l
commit
|
commitdiff
|
tree
2011-09-01
Mark Abra
h
a
m
Re
-
implemented g
e
nerati
n
g de
f
ault protei
n
index
gr
o
ups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraha
m
Adjusted
co
n
st
r
u
c
t
i
on o
f
defaul
t
inde
x
groups
commit
|
commitdiff
|
tree
2011-09-01
Mark
Abraham
Fixed co
m
ment
commit
|
commitdiff
|
tree
2011-08-23
M
a
rk Abrah
a
m
Fixed g_disre derefe
r
enc
i
ng c
r
commit
|
commitdiff
|
tree
2011-08-23
M
ark Abraham
Typo
f
ix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
Exp
l
a
i
ned
termina
l
residues and AMBER in pdb2
g
mx -h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abra
h
am
Made free e
n
ergy pert
u
r
bati
o
n work
w
i
th CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Ab
r
aham
F
i
xed outpu
t
b
u
g in
demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Streamline
d
small part
of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Ma
r
k Abraham
Reading a
.
g96
t
rajector
y
n
ow cau
s
es fat
a
l er
r
or
commit
|
commitdiff
|
tree
2011-07-11
Ma
r
k Abraham
F
i
x
s
ome identifier na
m
ing issues in last com
m
i
t
commit
|
commitdiff
|
tree
2011-07-11
Mark Ab
r
aham
Avo
i
d
e
d
some integer overfl
o
ws
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Clarif
i
ed use of
OPLS/AA
z
wit
t
erion termi
n
i
commit
|
commitdiff
|
tree
2011-07-08
M
ark
Abraha
m
Fixed improper fil
e
clos
e
wi
t
h GB and
mdrun
-debug
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Made pdb2gmx error mes
s
age l
e
ss cryp
t
ic
commit
|
commitdiff
|
tree
2011-06-29
Mark
Abraham
Rev
e
rt "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark Ab
r
a
ham
Improved erro
r
messa
g
e and documentati
o
n
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
dr
a
f
t
commit
|
commitdiff
|
tree
2011-06-21
Ma
r
k Abraham
Ex
p
anded LINCS
warni
n
g text
commit
|
commitdiff
|
tree
2011-06-07
Mark Abrah
a
m
Fi
x
ed spelling of reproducible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abrah
a
m
Added refere
n
ce to g_sas -h
commit
|
commitdiff
|
tree
2011-05-11
Mar
k
Abraham
Cleaned up g_sas help text
commit
|
commitdiff
|
tree
2011-05-09
Mark Abra
h
am
A
d
ded hint
about calling trjconv more than onc
e
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Abraham
Spaced out paragrap
h
s in t
r
j
conv help
commit
|
commitdiff
|
tree
2011-05-02
Mark
A
bra
h
am
Remo
v
ed dupli
c
ate definition of md_pri
n
t_warning()
commit
|
commitdiff
|
tree
2011-05-01
Mark
Abraham
F
i
xe
d
descripti
o
n of
.
mdp option to
"h-bond
s
"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Remo
v
e
d
unne
c
essar
y
#includes
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
b
raham
D
e
leted du
p
licate
d
code
commit
|
commitdiff
|
tree
2011-04-14
Mark A
b
ra
h
am
Moved various support func
t
ions fo
r
d
o
_md into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
b
raham
M
o
ved itera
t
ed
-
constraints code in
t
o
md
l
ib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved heuristic ne
i
ghbo
r
-list code in
t
o mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed co
d
e duplication
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraha
m
F
ixe
d
header #ifndef
test
commit
|
commitdiff
|
tree
2011-03-30
Mark Abraham
Removed
u
s
eless cons
t
qualifier
commit
|
commitdiff
|
tree
2011-03-30
M
a
rk Abraha
m
Suppressed Cyg
w
in
C-only compi
l
er wa
r
nin
g
s
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
Fixe
d
g_cluste
r
l
ogic error
commit
|
commitdiff
|
tree
2011-03-26
Mark
A
braham
Made gmx_rmpb
c
_t object functions not seg
f
a
ult
commit
|
commitdiff
|
tree
2011-03-26
Mark
Abraham
Fixed matio
.
c sfree(
)
that made DvdS
cr
y
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
A
dded
g
rompp note about
a
v
o
id
i
ng zero-step EM
commit
|
commitdiff
|
tree
2011-02-16
Mark Abraham
C
lar
i
fied
source of g
_
rmsf referenc
e
frame
commit
|
commitdiff
|
tree
2011-02-13
Mar
k
Ab
r
aham
Added workaround
f
or
F_GB13 duplicates
commit
|
commitdiff
|
tree
2011-02-13
Mark Abrah
a
m
Fixed erro
n
eo
u
s floating-point comparison
commit
|
commitdiff
|
tree
2011-02-12
M
a
r
k
Abra
h
am
Added note
a
bout doing repeat invocations
o
f genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraha
m
Removed ancient C
V
S t
a
g l
i
nes
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used some
s
pacing to make
code readable
commit
|
commitdiff
|
tree
2011-02-11
M
a
rk A
b
raha
m
Used symb
o
l
ic const
a
nt more
c
ons
i
stent
l
y
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Ma
d
e
the "multip
l
e settles
"
fatal error mor
e
helpful
commit
|
commitdiff
|
tree
2011-02-02
Mark Abra
h
a
m
Fixed minor issue w
i
th
repli
c
a
e
xchang
e
commit
|
commitdiff
|
tree
2011-01-28
M
a
r
k Abrah
a
m
Added fo
r
gotten
f
ile
commit
|
commitdiff
|
tree
2011-01-28
M
a
r
k Abraham
Turned g_options into a normal GROMACS
t
oo
l
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Re
n
amed s
r
c
/
to
o
ls
/
options
.
c
commit
|
commitdiff
|
tree
2011-01-28
M
ark Abraham
Improved grom
p
p docum
e
ntati
o
n
commit
|
commitdiff
|
tree
2011-01-25
Mark Abrah
a
m
Imp
r
oved genion -h
commit
|
commitdiff
|
tree
2011-01-25
Mar
k
A
b
raham
R
e
l
o
cate
d
some t_matrix documenta
t
ion
commit
|
commitdiff
|
tree
2011-01-25
Mark A
b
raham
I
mproved d
o
_
dssp -s
s
d
ump output
commit
|
commitdiff
|
tree
2011-01-25
Mar
k
Abraham
Improv
e
d
do_dssp -
s
c output
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
R
emove
g
_
highw
a
y from list of programs
commit
|
commitdiff
|
tree
2011-01-23
Mark Abrah
a
m
Impr
o
ved conversio
n
of document
a
tion to LaTeX
commit
|
commitdiff
|
tree
2011-01-23
Mark A
b
raham
I
m
proved consistency of
t
ext styl
e
usage
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Minor w
o
rding fixes
commit
|
commitdiff
|
tree
2011-01-23
M
ark Abraha
m
Moved options
.
c to t
o
ols
s
ubdir
commit
|
commitdiff
|
tree
2011-01-23
Ma
r
k
Ab
r
aham
cmake: ad
d
e
d b
a
ck gsl sup
p
ort
(GMX
_
GSL, disabled by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
Mark Abrah
a
m
A
d
ded NHE t
o
O
P
L
S
/AA pdb2gmx hyd
r
ogen
dat
a
base
commit
|
commitdiff
|
tree
2011-01-20
Mark Ab
r
aha
m
Made
gmxdump e
r
r
or message c
l
earer
.
commit
|
commitdiff
|
tree
2011-01-18
Mark
Abr
a
ham
I
m
proved
.
mdp file
comment about
the
'define' fi
e
ld
commit
|
commitdiff
|
tree
2011-01-17
Mark
Abraham
Fix Angs
t
ro
m
<=>
n
m error in docum
e
ntati
o
n
commit
|
commitdiff
|
tree
2011-01-13
Mark Abraham
M
a
de src/kern
e
l
/
repl_ex
.
c legible
commit
|
commitdiff
|
tree
2011-01-07
M
ark Abraha
m
Added n
o
te that g_msd -mo
l
d
o
es tre
a
t PBC (by
m
a
king
.
.
.
commit
|
commitdiff
|
tree
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