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Minor formatting fixes to .mdp option documentation
2012-02-24
M
ark Abr
a
ham
M
i
nor f
o
rmatt
i
ng fixes to
.
mdp option doc
u
mentation
commit
|
commitdiff
|
tree
2012-02-10
Mark Abraham
Fixed g_sham using more than three dime
n
s
ions
commit
|
commitdiff
|
tree
2012-02-10
M
ark Abraham
Integer multiplicatio
n
that
checks fo
r
over
f
low
commit
|
commitdiff
|
tree
2012-02-01
Mar
k
A
b
ra
h
am
Fixed
t
rjconv
-sub
commit
|
commitdiff
|
tree
2012-02-01
Mark Ab
r
aham
Fixed erro
r
message
t
o
id
e
nti
f
y the correct file
commit
|
commitdiff
|
tree
2012-02-01
M
ark Ab
r
aham
Improved error message
commit
|
commitdiff
|
tree
2012-01-31
Ma
r
k Abr
a
ham
Mer
g
e "Corr
e
cted us
e
o
f
?: in conditi
o
nal" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark Abra
h
am
Made error message even more exp
l
ici
t
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abraham
Correcte
d
use of ?: i
n
condition
a
l
commit
|
commitdiff
|
tree
2012-01-10
Mark Abra
h
am
Fix
e
d use
of isfinite and _i
s
finite
commit
|
commitdiff
|
tree
2012-01-04
Mark Abraham
Added
CMake T
o
olchain fi
l
e for BlueGene/P
commit
|
commitdiff
|
tree
2011-12-29
M
a
rk Ab
r
aham
Documented the functi
o
n
of g_clus
t
e
r -cl -
n
oav
commit
|
commitdiff
|
tree
2011-12-14
Ma
r
k Abraham
Re-
f
i
xed s
t
a
tic
l
ink
i
ng of maths libra
r
ie
s
under UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
Relaxe
d
so
m
e assum
p
tio
n
s about trajectory times
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Only
anal
y
se angl
e
transiti
o
ns for dihedral
a
ngles
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
A
dded
protective prepro
c
e
ss
o
r directives
commit
|
commitdiff
|
tree
2011-11-23
Ma
r
k Abraham
Fixed g_angl
e
-f -or to copy
t
imes f
r
om -f to
-
or
commit
|
commitdiff
|
tree
2011-11-02
Mar
k
Abraham
Fix for GB
,
do
u
ble, SS
E
2 and optimize
d
kernel
s
commit
|
commitdiff
|
tree
2011-11-01
Mark
Abraham
T
r
igger
correct kernels un
d
e
r
C
ygwin
commit
|
commitdiff
|
tree
2011-10-27
Mark A
b
rah
a
m
Made readi
n
g of binary matrices m
o
r
e
robust
commit
|
commitdiff
|
tree
2011-10-19
M
a
rk Ab
r
aha
m
Co
r
rec
t
e
d charg
e
of CHAR
M
M zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
R
emoved erroneou
s
us
e
of MASSV on
BlueGene
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Fix
e
s
for
G
B kernel
commit
|
commitdiff
|
tree
2011-09-27
Mark Ab
r
aha
m
Added tip for conver
t
ing
.
xpm to
somethin
g
u
s
e
f
u
l
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dropped some hints in the
documen
t
ation
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraha
m
Removed CMake warning for recent Op
e
nMPI
ver
s
ions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Fix trjconv -sub
commit
|
commitdiff
|
tree
2011-09-15
Mark Abrah
a
m
Warnin
g
about
trj
c
onv -sub needing many
fi
l
es open
commit
|
commitdiff
|
tree
2011-09-15
Mark Ab
r
aham
g_sha
m
-mdata is an input fi
l
e, not output file
commit
|
commitdiff
|
tree
2011-09-14
Mark Abra
h
am
F
o
r
m
at warni
n
g
bett
e
r
commit
|
commitdiff
|
tree
2011-09-13
M
a
rk A
b
raham
F
i
x pdb2
g
mx
-de
b
u
g
and
.
hdb
f
iles
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abrah
a
m
Fix for C
M
ake finding LAPA
C
K
commit
|
commitdiff
|
tree
2011-09-13
Mark Abr
a
ham
Ad
d
ed ACE
a
n
d
CT3 to CHARMM27 a
m
i
n
o
a
cids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fixed char
g
e gro
u
ps of CH
A
RMM27 DNA
/
RNA terminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abr
a
ham
Fixes fo
r
CMake fi
n
ding FORTRAN library names on POW
E
R6
commit
|
commitdiff
|
tree
2011-09-06
Mark
Abraham
Fix bug w
i
th l
a
rge ints with
o
ut MP
I
_IN_P
L
ACE
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Made grompp n
o
t
e
about no
n
-zero charge mo
r
e
useful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Re-implement
e
d
gene
r
ating defau
l
t protein
i
ndex groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Adjust
e
d co
n
struction of defa
u
lt
i
n
de
x
groups
commit
|
commitdiff
|
tree
2011-09-01
M
a
rk
Abraham
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark Ab
r
aham
Fix
e
d g_disre dereferenc
i
ng cr
commit
|
commitdiff
|
tree
2011-08-23
Mark A
b
ra
h
am
Typ
o
fix
commit
|
commitdiff
|
tree
2011-08-19
Mar
k
Abraham
Expl
a
ined t
e
rm
i
nal residues
and AMBER in pdb2gmx
-
h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abraham
Made free
e
nerg
y
p
e
rturbation
work
w
ith CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abraham
Fixed
o
u
tput b
u
g in demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraham
Str
e
a
m
l
i
ned small part
of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
M
a
rk Abraham
R
eading a
.
g96 trajectory now c
a
uses fatal error
commit
|
commitdiff
|
tree
2011-07-11
Mark
Abraham
Fix some
i
dentifier
n
aming
i
ssues in
l
a
st
c
ommit
commit
|
commitdiff
|
tree
2011-07-11
Mar
k
Abraham
A
v
oided
some integer overflows
commit
|
commitdiff
|
tree
2011-07-08
Ma
r
k
A
braham
Clarified use of
OPLS/AA zwitterio
n
termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abra
h
am
F
ixe
d
imp
r
oper fil
e
c
lose wit
h
G
B and
m
dru
n
-debug
commit
|
commitdiff
|
tree
2011-07-08
Mark Abrah
a
m
Made pdb2g
m
x error message less cryp
t
i
c
commit
|
commitdiff
|
tree
2011-06-29
Mark Abra
h
am
Revert "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark A
b
raham
I
m
pro
v
ed erro
r
message and
d
ocumen
t
ation
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
A
b
r
ah
a
m
draft
commit
|
commitdiff
|
tree
2011-06-21
Ma
r
k Abraham
E
x
pa
n
ded LINCS warn
i
ng
text
commit
|
commitdiff
|
tree
2011-06-07
Mark Abr
a
ham
Fixed spe
l
ling
of repro
d
ucible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Added refere
n
ce to g_sas -h
commit
|
commitdiff
|
tree
2011-05-11
M
a
r
k
Ab
r
aham
Cl
e
an
e
d up g
_
sas h
e
lp text
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k A
b
raham
A
dded h
i
nt
a
bout calling tr
j
co
n
v mor
e
t
han
once
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
S
p
a
ced out paragraphs in trjc
o
nv help
commit
|
commitdiff
|
tree
2011-05-02
Mar
k
A
braham
Remove
d
dupli
c
at
e
defin
i
tion of
m
d_print_
w
arning
(
)
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraham
Fixed description of
.
m
dp
option to "
h
-b
o
nds"
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Removed unnecessary #inc
l
udes
commit
|
commitdiff
|
tree
2011-04-14
Mark A
b
raham
Deleted duplicated code
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
Moved various
su
p
port functions for do_md int
o
m
d
lib
commit
|
commitdiff
|
tree
2011-04-14
M
ark Abraham
Moved iterate
d
-constraints code i
n
to m
d
li
b
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abrah
a
m
Move
d
heuristi
c
neighbor
-
list
c
od
e
into
m
dl
i
b
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k A
b
r
a
ham
Fix
e
d cod
e
duplication
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
F
ixed header #ifndef
t
est
commit
|
commitdiff
|
tree
2011-03-30
Mark Ab
r
a
h
am
Rem
o
ved use
l
ess co
n
st qualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark
A
braham
Suppressed
C
ygwin C-only
compiler warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark
A
braha
m
F
ixed g_cluster logic error
commit
|
commitdiff
|
tree
2011-03-26
M
ark
A
braham
Made gmx_rmpb
c
_t object funct
i
o
ns not segfault
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraha
m
Fixed matio
.
c
sfree() that
m
a
d
e
D
vdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraha
m
Added
grompp note about avoiding zero-step
EM
commit
|
commitdiff
|
tree
2011-02-16
Ma
r
k Abraha
m
Clarifie
d
source of g_rmsf
re
f
erence frame
commit
|
commitdiff
|
tree
2011-02-13
Mark
A
b
r
aham
A
dded worka
r
ound for F_GB13 duplic
a
tes
commit
|
commitdiff
|
tree
2011-02-13
Mark Abr
a
ham
F
i
xed erroneo
u
s fl
o
atin
g
-poin
t
comparison
commit
|
commitdiff
|
tree
2011-02-12
Mark Abra
h
am
Ad
d
ed note about doing repeat invocation
s
of genbox
commit
|
commitdiff
|
tree
2011-02-11
M
a
rk Abraham
Removed a
n
cient CVS tag lin
e
s
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Us
e
d some spacin
g
t
o
make co
d
e
readable
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraha
m
Used symbolic const
a
nt more
consist
e
ntly
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
M
ade the "
m
ultipl
e
sett
l
es" fat
a
l er
r
or
m
o
r
e
helpf
u
l
commit
|
commitdiff
|
tree
2011-02-02
Mark Ab
r
a
h
am
Fi
x
ed minor issu
e
with
r
eplica exchange
commit
|
commitdiff
|
tree
2011-01-28
Mark
Abr
a
ham
Added
f
orgotten file
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
T
urne
d
g_optio
n
s into a normal G
R
OMACS
t
ool
commit
|
commitdiff
|
tree
2011-01-28
M
ark Abr
a
ham
Renamed src/tools/
o
pt
i
o
n
s
.
c
commit
|
commitdiff
|
tree
2011-01-28
M
a
rk Abraham
I
mproved grompp document
a
tion
commit
|
commitdiff
|
tree
2011-01-25
Mark Ab
r
aham
Improved
g
enion -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Relocated som
e
t_matri
x
documentatio
n
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraha
m
Improved do_dssp -ssdump output
commit
|
commitdiff
|
tree
2011-01-25
Ma
r
k Abraham
Improved do_dssp -
s
c output
commit
|
commitdiff
|
tree
2011-01-23
Mar
k
Ab
r
aham
Remove g_highway fr
o
m list o
f
pr
o
grams
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk Abraham
Improved con
v
ersion of documentation t
o
L
aTeX
commit
|
commitdiff
|
tree
2011-01-23
Mark Ab
r
aham
I
m
proved
c
o
nsistency of
text style
u
sage
commit
|
commitdiff
|
tree
2011-01-23
M
ar
k
Abrah
a
m
M
inor
wo
r
ding fixes
commit
|
commitdiff
|
tree
2011-01-23
Mark
Abraha
m
Moved op
t
ions
.
c to
t
oo
l
s subdi
r
commit
|
commitdiff
|
tree
2011-01-23
Mark Abra
h
am
c
ma
k
e: added back gsl su
p
p
o
rt (GMX_GS
L
,
di
s
abled
by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
Mark Abraham
Added
NHE to OPLS
/
AA pdb2gmx hyd
r
ogen da
t
abase
commit
|
commitdiff
|
tree
next