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Added CMake Toolchain file for BlueGene/P
2012-01-04
Ma
r
k A
b
raham
A
d
de
d
CMa
k
e
T
o
o
lchain file
f
or BlueGene/P
commit
|
commitdiff
|
tree
2011-12-14
Mark A
b
raham
R
e-fixe
d
static
l
inking of maths
l
ibra
r
ies
und
e
r
U
NIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
Rel
a
xed s
o
m
e a
s
sumptions about trajectory ti
m
es
commit
|
commitdiff
|
tree
2011-11-24
M
ark Abraham
Only a
n
al
y
se angle transitions
f
or di
h
edral ang
l
e
s
commit
|
commitdiff
|
tree
2011-11-24
Mar
k
Abraham
A
d
ded protective pr
e
proc
e
ssor directiv
e
s
commit
|
commitdiff
|
tree
2011-11-23
Mar
k
Abraham
Fixed
g
_a
n
gle -f -or to copy times from -f to
-or
commit
|
commitdiff
|
tree
2011-11-02
Mark Abra
h
am
F
ix fo
r
GB, double, SSE2 and opt
i
miz
e
d k
e
rnels
commit
|
commitdiff
|
tree
2011-11-01
Mark Abraham
Tr
i
gg
e
r
correct
kernels
under Cygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abraham
Made readin
g
of binary
m
atrices
m
or
e
robust
commit
|
commitdiff
|
tree
2011-10-19
M
a
r
k Ab
r
aham
Corrected charge
of C
H
ARMM zinc
i
on
to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abra
h
am
Remov
e
d err
o
n
e
ous u
s
e of MASSV on Blu
e
Gene
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Fixes for GB kernel
commit
|
commitdiff
|
tree
2011-09-27
M
ar
k
Abrah
a
m
Added tip for c
o
nve
r
t
ing
.
xpm to some
t
hing usef
u
l
commit
|
commitdiff
|
tree
2011-09-26
Mark Abra
h
am
Dropped some hints in the documentation
commit
|
commitdiff
|
tree
2011-09-26
Mark Abra
h
am
Removed CMake warning for rece
n
t OpenMPI versions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Fix
trjco
n
v -sub
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
W
a
rni
n
g a
b
out tr
j
con
v
-su
b
needing many f
i
les
op
e
n
commit
|
commitdiff
|
tree
2011-09-15
Mark Abrah
a
m
g_
s
ham -mdata is an
input
f
ile, not output fi
l
e
commit
|
commitdiff
|
tree
2011-09-14
Mark Abraham
Format warnin
g
better
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abraham
Fi
x
pdb2
g
mx -d
e
bug and
.
h
db fi
l
es
commit
|
commitdiff
|
tree
2011-09-13
Mar
k
A
braham
Fix
for CMake findin
g
LAP
A
CK
commit
|
commitdiff
|
tree
2011-09-13
Ma
r
k
A
bra
h
am
Added A
C
E and CT3 to CH
A
RMM27
a
mi
n
oacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark Abra
h
am
Fixe
d
charge
g
r
oups of CHARMM27 DNA/R
N
A terminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
F
ixes
fo
r
C
Make findi
n
g
F
O
R
TRAN library na
m
es on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Ab
r
ah
a
m
Fix bug with large ints without MPI_IN
_
PLACE
commit
|
commitdiff
|
tree
2011-09-01
M
ark
Abraham
Made grompp
note about non
-
zero ch
a
rge more usef
u
l
commit
|
commitdiff
|
tree
2011-09-01
M
a
r
k
A
b
raham
Re-i
m
p
l
e
m
e
nted gene
r
ating default
prot
e
in index gro
u
ps
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Ad
j
ust
e
d cons
t
ruct
i
on of d
e
fault index groups
commit
|
commitdiff
|
tree
2011-09-01
M
ark Abraham
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark A
b
rah
a
m
Fixed g_disre dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark A
b
r
a
h
am
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abraham
E
xp
l
ained te
r
mina
l
residues and AMBE
R
in pd
b
2gmx -h
commit
|
commitdiff
|
tree
2011-08-16
M
ark Abraham
Made fr
e
e energy p
e
r
t
urbation wor
k
w
ith CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abr
a
ham
Fixed
output
b
u
g in de
m
ux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Streamlined
s
ma
l
l part of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark Abraham
R
eading a
.
g96 trajectory n
o
w causes fatal
error
commit
|
commitdiff
|
tree
2011-07-11
Mark Abr
a
ham
Fix some identi
f
ier naming
iss
u
es
i
n last
c
ommit
commit
|
commitdiff
|
tree
2011-07-11
Mar
k
Abraham
Avoided some
i
nteger
o
v
erflows
commit
|
commitdiff
|
tree
2011-07-08
Mark
Abraham
Cla
r
ified
u
se o
f
O
P
LS/AA
zwitterion termini
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk
A
braham
Fi
x
ed impro
p
er file close with GB and m
d
run -debug
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk
A
br
a
ham
Made pdb2g
m
x error messa
g
e
l
e
ss cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark
Abra
h
am
Re
v
e
r
t "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark A
b
ra
h
a
m
Improved error
m
essage
and docum
e
n
tation
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
draft
commit
|
commitdiff
|
tree
2011-06-21
Ma
r
k Abra
h
a
m
E
x
panded LINCS wa
r
ning text
commit
|
commitdiff
|
tree
2011-06-07
Mar
k
A
b
r
a
h
am
F
i
xed spelling of reproducible
commit
|
commitdiff
|
tree
2011-05-11
Ma
r
k
Abr
a
ham
A
dded ref
e
rence to
g_sa
s
-h
commit
|
commitdiff
|
tree
2011-05-11
M
a
r
k Abraham
Cleaned up
g
_
s
as help text
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
A
dded h
i
nt abo
u
t call
i
ng tr
j
conv
mo
r
e
t
han once
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Abraham
Spaced out par
a
graphs i
n
t
rjc
o
nv
h
elp
commit
|
commitdiff
|
tree
2011-05-02
Mark Abraham
Remov
e
d duplicat
e
definition
of md_print_warni
n
g
()
commit
|
commitdiff
|
tree
2011-05-01
M
a
rk Ab
r
aham
F
ixe
d
descri
p
tio
n
of
.
mdp option to "h-bon
d
s"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Rem
o
ved unnec
e
ssary #includes
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abraham
D
e
leted
duplicated
c
o
d
e
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k
A
b
r
aham
M
oved various s
u
pport functions for do_md
i
nto mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
br
a
ham
M
o
ved iterat
e
d
-c
o
n
s
tr
a
ints
code
into mdlib
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
Moved heuristic n
e
ighbor-li
s
t code into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mar
k
Abra
h
am
F
ixed code dupl
i
cation
commit
|
commitdiff
|
tree
2011-04-14
Mar
k
Abraham
Fixed header #ifndef test
commit
|
commitdiff
|
tree
2011-03-30
Mark A
b
raham
R
em
o
v
e
d useles
s
cons
t
qu
a
li
f
ier
commit
|
commitdiff
|
tree
2011-03-30
M
ark Abra
h
am
Sup
p
r
essed Cygwin C-only compile
r
wa
r
nings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abr
a
ham
Fixed
g
_
c
lu
s
t
e
r logic error
commit
|
commitdiff
|
tree
2011-03-26
Ma
r
k
A
braham
Ma
d
e g
m
x_rmpbc
_
t
object functions
n
ot seg
f
ault
commit
|
commitdiff
|
tree
2011-03-26
Mark
Abra
h
am
Fix
e
d
m
a
tio
.
c sfree(
)
t
h
at
made DvdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added grompp note
a
bou
t
av
o
idi
n
g zero-s
t
ep EM
commit
|
commitdiff
|
tree
2011-02-16
Ma
r
k
Ab
r
aha
m
Clarifi
e
d so
u
rce of g_rmsf refer
e
nce
f
rame
commit
|
commitdiff
|
tree
2011-02-13
M
a
rk A
b
ra
h
am
Added workaround for F_GB13 dupli
c
a
t
es
commit
|
commitdiff
|
tree
2011-02-13
Mark Abr
a
ham
Fixed erroneous flo
a
ti
n
g
-point compa
r
iso
n
commit
|
commitdiff
|
tree
2011-02-12
Mark
Abra
h
am
Added note about d
o
ing repeat
i
nvocati
o
ns of gen
b
ox
commit
|
commitdiff
|
tree
2011-02-11
M
a
r
k
Abr
a
h
a
m
R
emoved anc
i
ent CVS t
a
g
l
i
nes
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used some spacing
to make code reada
b
le
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Used symbolic constant more co
n
si
s
tently
commit
|
commitdiff
|
tree
2011-02-11
Mark Abra
h
am
Ma
d
e
the
"multipl
e
settles"
fatal er
r
o
r m
o
re helpfu
l
commit
|
commitdiff
|
tree
2011-02-02
Mark A
b
raham
F
ixed minor issue wit
h
repli
c
a exchange
commit
|
commitdiff
|
tree
2011-01-28
Mark A
b
ra
h
am
Ad
d
ed forgotten fi
l
e
commit
|
commitdiff
|
tree
2011-01-28
Mar
k
Abraha
m
Turn
e
d
g_opt
i
ons into a normal GR
O
M
ACS too
l
commit
|
commitdiff
|
tree
2011-01-28
Mar
k
Abraham
Ren
a
med
src/too
l
s
/option
s
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mark
Abraham
Improved grompp doc
u
mentatio
n
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved gen
i
o
n
-h
commit
|
commitdiff
|
tree
2011-01-25
M
a
r
k Abrah
a
m
Relocated some t_matrix documentat
i
o
n
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved do_dssp -ssd
u
mp output
commit
|
commitdiff
|
tree
2011-01-25
Mark
A
braham
Improved do_dssp -sc output
commit
|
commitdiff
|
tree
2011-01-23
Mark
Ab
r
a
h
am
R
e
move g
_
highway fro
m
list of programs
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Impro
v
ed co
n
version of documentation to LaTeX
commit
|
commitdiff
|
tree
2011-01-23
Mar
k
A
b
raham
Impro
v
ed consistenc
y
of text styl
e
u
s
ag
e
commit
|
commitdiff
|
tree
2011-01-23
Mark
Abra
h
am
M
i
n
o
r wo
r
ding
f
i
xes
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Moved options
.
c to
t
ools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
cmake:
a
d
ded
back gsl sup
p
ort
(
GMX_GSL, disabled by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
Mark
A
braham
Ad
d
ed NHE t
o
O
PLS
/
AA pdb2gmx hydr
o
gen databa
s
e
commit
|
commitdiff
|
tree
2011-01-20
Mar
k
Abr
a
ham
Made gmxdump er
r
or message clearer
.
commit
|
commitdiff
|
tree
2011-01-18
M
a
rk
A
b
r
a
ham
Improved
.
md
p
f
i
le comment about
the 'define' field
commit
|
commitdiff
|
tree
2011-01-17
Mark Abraham
Fix Angstrom <=> nm error in docume
n
tation
commit
|
commitdiff
|
tree
2011-01-13
Mark Abraham
Made src/kernel/repl_e
x
.
c legible
commit
|
commitdiff
|
tree
2011-01-07
Mar
k
Abraham
Added
note
that g_msd -mol does tre
a
t PBC
(
by
m
aking
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Ma
r
k Abra
h
am
Implemented
effective te
s
t for MPI_IN_PLACE,
thanks
.
.
.
commit
|
commitdiff
|
tree
2011-01-06
Mar
k
A
b
raham
Stop CMa
k
e defaulting to tu
r
ning off
com
p
i
le
r
warning
s
.
.
.
commit
|
commitdiff
|
tree
2010-12-06
Ma
r
k Abr
a
h
am
Added comme
n
t
s and workaroun
d
for
IBM's BlueGene(/L
.
.
.
commit
|
commitdiff
|
tree
2010-11-22
Mark Abraha
m
Added a h
i
nt
t
o the document
a
tion fo
r
creating
.
t
pr
.
.
.
commit
|
commitdiff
|
tree
2010-11-12
Mark Abraham
Mino
r
t
r
j
con
v
documentation form
a
tting fix
commit
|
commitdiff
|
tree
2010-11-12
Ma
r
k Abr
a
ham
g_densm
a
p
-od writ
e
s a
.
dat file and prevents w
r
itin
g
.
.
.
commit
|
commitdiff
|
tree
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