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Fixed trjconv -sub
2012-02-01
Mark Abra
h
a
m
Fixed trj
c
o
n
v -sub
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Merge "
C
orrected us
e
of ?: in conditi
o
n
al" into r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
Made err
o
r messa
g
e even more explicit
commit
|
commitdiff
|
tree
2012-01-31
M
a
rk Ab
r
a
h
a
m
Corrected
u
s
e
of ?: in condi
t
ional
commit
|
commitdiff
|
tree
2012-01-10
M
ark Abraham
F
i
xed use of
i
sfinite and _isf
i
n
i
te
commit
|
commitdiff
|
tree
2012-01-04
Mark Abraham
Added CMa
k
e
T
ool
c
hain fi
l
e for BlueGene/P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abraham
Documen
t
ed
the fu
n
c
t
ion of
g_cl
u
ster
-cl -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark Abraham
Re-fixed
s
tatic
l
in
k
ing of maths librarie
s
under UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
Relax
e
d
s
o
m
e a
s
sumptions about traje
c
tory t
i
mes
commit
|
commitdiff
|
tree
2011-11-24
Mark Abrah
a
m
Only a
n
alyse angle transiti
o
ns for dihedral angles
commit
|
commitdiff
|
tree
2011-11-24
Mark A
b
raham
Added pro
t
ect
i
v
e
preprocessor di
r
ectives
commit
|
commitdiff
|
tree
2011-11-23
Mark Abrah
a
m
F
i
xed g_angle -f -or t
o
c
o
py
ti
m
es from -
f
to -or
commit
|
commitdiff
|
tree
2011-11-02
Mark Abr
a
ham
Fix for GB,
d
ouble, SSE2 and
o
ptimized kernels
commit
|
commitdiff
|
tree
2011-11-01
Mark Abraham
T
r
igger c
o
rrect
k
ernels under C
y
gwin
commit
|
commitdiff
|
tree
2011-10-27
Mark Abraham
M
a
de reading of binary matrices more robust
commit
|
commitdiff
|
tree
2011-10-19
Mark A
b
rah
a
m
Corrected
c
harge of CHARM
M
zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
M
ark
A
b
r
aha
m
Re
m
o
ved erroneous use of MASS
V
on BlueGe
n
e
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Fixes f
o
r GB ke
r
ne
l
commit
|
commitdiff
|
tree
2011-09-27
Mark
A
braha
m
Added tip for conv
e
rt
i
ng
.
xpm to
so
m
eth
i
ng us
e
ful
commit
|
commitdiff
|
tree
2011-09-26
Mark Abrah
a
m
Dr
o
pped some hints in the docume
n
tation
commit
|
commitdiff
|
tree
2011-09-26
M
a
rk Abr
a
ham
Remo
v
ed CM
a
ke warning for re
c
e
n
t O
p
enMP
I
v
ersions
commit
|
commitdiff
|
tree
2011-09-15
Mark Abr
a
ham
Fix trjconv -su
b
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
Warning
a
bou
t
t
r
jc
o
nv -s
u
b
n
e
eding many fil
e
s op
e
n
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
b
raham
g_sham -mdata i
s
an input file,
n
ot output file
commit
|
commitdiff
|
tree
2011-09-14
Mark A
b
raham
Format wa
r
n
i
ng better
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
raham
Fix pdb2gmx -d
e
bug and
.
h
db files
commit
|
commitdiff
|
tree
2011-09-13
Mark
Abrah
a
m
Fix for CM
a
ke f
i
ndi
n
g LAPACK
commit
|
commitdiff
|
tree
2011-09-13
Mar
k
Abraham
Ad
d
e
d ACE
and CT3
to CHARMM27
a
minoa
c
ids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark
A
b
r
aham
Fixed charge g
r
oups of CHARMM27 DNA/RNA terminal H
commit
|
commitdiff
|
tree
2011-09-13
Mark
Abraham
F
ixes fo
r
CMake finding FORTR
A
N library names on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Abraham
Fix bug with large int
s
without MPI_
I
N_PLACE
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Made
gr
o
mpp note about non-zero charge more
useful
commit
|
commitdiff
|
tree
2011-09-01
Mark A
b
raham
Re-imple
m
ented
g
e
nerati
n
g default pr
o
tein index
groups
commit
|
commitdiff
|
tree
2011-09-01
Mar
k
A
bra
h
am
Adjust
e
d co
n
struction of default
i
ndex groups
commit
|
commitdiff
|
tree
2011-09-01
M
a
rk Abraha
m
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraha
m
Fi
x
ed
g
_
disre dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
M
a
rk
A
br
a
ham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Mark Abrah
a
m
Exp
l
ained termi
n
a
l
residues an
d
A
MBER in pdb2
g
mx -h
commit
|
commitdiff
|
tree
2011-08-16
Mar
k
A
brah
a
m
M
a
d
e free energy perturbati
o
n work
w
ith CM
A
P
commit
|
commitdiff
|
tree
2011-08-03
M
a
rk Abra
h
am
Fixed output bug in
demux
.
p
l
commit
|
commitdiff
|
tree
2011-07-17
Mark
A
b
r
aham
St
r
eamlin
e
d small par
t
of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mar
k
Abraha
m
Re
a
din
g
a
.
g96
t
rajectory now caus
e
s fatal err
o
r
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Fi
x
some identifi
e
r nami
n
g issues
i
n last c
o
mm
i
t
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Avoided some integer overfl
o
ws
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
aham
Clarified use of OP
L
S
/
AA zwitt
e
rion termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abr
a
ham
Fixed i
m
proper
f
ile close wit
h
GB and
mdr
u
n -debug
commit
|
commitdiff
|
tree
2011-07-08
Mark Abra
h
a
m
Made pdb2gmx error
m
essage les
s
cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mark
A
braham
R
e
ver
t
"dra
f
t"
commit
|
commitdiff
|
tree
2011-06-29
Ma
r
k A
b
r
a
ham
I
m
pro
v
ed er
r
o
r
message
a
nd documentation
commit
|
commitdiff
|
tree
2011-06-29
Mark
Abraham
draft
commit
|
commitdiff
|
tree
2011-06-21
M
a
rk Abraham
Expanded LIN
C
S w
a
r
n
i
n
g t
e
xt
commit
|
commitdiff
|
tree
2011-06-07
Ma
r
k Abraham
Fixed spellin
g
o
f
reproducible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abra
h
a
m
Ad
d
ed reference to g_sas
-
h
commit
|
commitdiff
|
tree
2011-05-11
Mark
Abra
h
am
Cleaned u
p
g_sas he
l
p text
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
Added h
i
n
t
a
bout cal
l
ing t
r
jconv
m
o
r
e than once
commit
|
commitdiff
|
tree
2011-05-09
Mark
Abra
h
am
Spaced out paragr
a
phs in
t
rjconv he
l
p
commit
|
commitdiff
|
tree
2011-05-02
Mark
A
b
raham
R
emoved duplicate definition of
m
d_prin
t
_w
a
rning
(
)
commit
|
commitdiff
|
tree
2011-05-01
Ma
r
k Abraham
Fixe
d
d
e
scriptio
n
of
.
mdp op
t
ion to "h-bon
d
s
"
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abr
a
ham
Removed unnec
e
ssary #includes
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
b
raha
m
Deleted
d
up
l
i
c
ated code
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
M
oved v
a
rious support functi
o
ns for do_md
into mdli
b
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
M
oved iterated-constraints code i
n
to
m
dlib
commit
|
commitdiff
|
tree
2011-04-14
Mark
A
braham
Move
d
heurist
i
c n
e
ighbor-list
code
i
n
to mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fix
e
d c
o
d
e
duplic
a
tion
commit
|
commitdiff
|
tree
2011-04-14
Mark Abrah
a
m
Fixed
h
e
ade
r
#ifndef test
commit
|
commitdiff
|
tree
2011-03-30
Mar
k
Abraham
Remov
e
d usel
e
ss
const qualifier
commit
|
commitdiff
|
tree
2011-03-30
M
ark Abr
a
ham
Suppr
e
ssed
Cygwin
C
-only compile
r
warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abraham
F
ixed g_cluste
r
logic error
commit
|
commitdiff
|
tree
2011-03-26
Ma
r
k Abraha
m
Made gmx_rmp
b
c_t ob
j
ect functions not segf
a
ult
commit
|
commitdiff
|
tree
2011-03-26
Mark
A
b
r
ah
a
m
Fixed matio
.
c
s
free() tha
t
made Dvd
S
cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added grompp note
ab
o
ut a
v
oid
i
ng
z
ero-step EM
commit
|
commitdiff
|
tree
2011-02-16
M
ark Abraham
C
l
arifie
d
source
of g_rmsf reference
frame
commit
|
commitdiff
|
tree
2011-02-13
M
ark Abrah
a
m
Added worka
r
ou
n
d for
F
_GB13 dupl
i
cates
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraham
Fixed erroneous flo
a
t
ing-point comparison
commit
|
commitdiff
|
tree
2011-02-12
M
a
rk
Abraham
Added note about doing repeat invocations
of genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark
A
b
r
a
ha
m
Removed
ancient CVS
ta
g
lines
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
raham
Used some spacin
g
to make code r
e
ada
b
le
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
U
s
ed
symbolic constant more con
s
istently
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
raham
Made the "mul
t
i
ple
settles" fatal error
more helpful
commit
|
commitdiff
|
tree
2011-02-02
Mark A
b
raha
m
Fix
e
d mino
r
i
s
sue
w
ith
r
eplica exchange
commit
|
commitdiff
|
tree
2011-01-28
Mark Ab
r
a
ham
Added forgotten file
commit
|
commitdiff
|
tree
2011-01-28
Mark Abr
a
ham
Tu
r
n
ed g_options into a
normal GROMACS tool
commit
|
commitdiff
|
tree
2011-01-28
Mark
A
b
r
aham
Renamed src/tools/options
.
c
commit
|
commitdiff
|
tree
2011-01-28
M
ark Abra
h
am
Improved grompp
documentation
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Improved g
e
nion -h
commit
|
commitdiff
|
tree
2011-01-25
Mark Abr
a
ham
Rel
o
cated s
o
me t_m
a
tr
i
x
d
ocumentation
commit
|
commitdiff
|
tree
2011-01-25
M
ark Abraham
Im
p
roved do
_
dssp -ssdump out
p
ut
commit
|
commitdiff
|
tree
2011-01-25
Mark Abraham
Impro
v
ed do_dssp
-
sc output
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk A
b
raham
Remove g_
h
i
g
h
w
ay from list of pr
o
grams
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk Abraha
m
Improved conversion
of docu
m
entation
t
o LaTeX
commit
|
commitdiff
|
tree
2011-01-23
M
a
rk
A
braham
Imp
r
oved consistency of
t
e
x
t style usage
commit
|
commitdiff
|
tree
2011-01-23
M
ar
k
Abraham
Minor wo
r
ding fixes
commit
|
commitdiff
|
tree
2011-01-23
M
ark
A
b
r
a
h
am
Mov
e
d options
.
c
to tools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark
Ab
r
aham
cmake: added back g
s
l
s
u
pport
(GMX_GS
L
, disabl
e
d by
.
.
.
commit
|
commitdiff
|
tree
2011-01-20
M
a
rk Abra
h
am
Adde
d
NHE to OPL
S
/AA pdb2gmx
h
ydrogen database
commit
|
commitdiff
|
tree
2011-01-20
Mark Abra
h
am
Made gmxdump error me
s
sa
g
e c
l
ear
e
r
.
commit
|
commitdiff
|
tree
2011-01-18
Mark
A
braham
Improved
.
mdp file comm
e
nt about the 'define' field
commit
|
commitdiff
|
tree
2011-01-17
M
a
rk Abr
a
ham
F
ix Angstrom <=> nm error in documentation
commit
|
commitdiff
|
tree
2011-01-13
Mar
k
A
braham
Mad
e
s
r
c/
k
ernel/repl_
e
x
.
c
legible
commit
|
commitdiff
|
tree
2011-01-07
Mark
Abra
h
am
A
d
d
e
d note tha
t
g_m
s
d
-mol does
t
r
eat PBC (by m
a
king
.
.
.
commit
|
commitdiff
|
tree
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