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Fixed trjconv -sub
2012-02-01
Mark Abraham
Fix
e
d trjconv -sub
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Ab
r
aham
Made
erro
r
me
s
sage even more expl
i
cit
commit
|
commitdiff
|
tree
2012-01-31
Mark Abrah
a
m
Co
r
rected use of
?
: in con
d
i
t
ional
commit
|
commitdiff
|
tree
2012-01-10
Mark
A
bra
h
am
Fixed use of i
s
finit
e
and _isfinite
commit
|
commitdiff
|
tree
2012-01-04
Ma
r
k Abraham
Added C
M
ake T
o
olchain file for BlueGene/P
commit
|
commitdiff
|
tree
2011-12-29
Mark Abr
a
ham
Docu
m
ented the
f
u
n
c
t
ion
of
g_cluster -cl -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark Abraham
Re-fixed sta
t
ic l
i
nki
n
g of maths librari
e
s unde
r
UN
I
X
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
R
e
lax
e
d some
a
s
sumptions about trajec
t
ory t
i
mes
commit
|
commitdiff
|
tree
2011-11-23
Mark Abraham
Fixed g_ang
l
e -f -or to copy times fr
o
m -f
t
o -or
commit
|
commitdiff
|
tree
2011-11-02
Ma
r
k Abraha
m
Fix for GB, d
o
uble, SSE2 a
n
d optimized kern
e
ls
commit
|
commitdiff
|
tree
2011-11-01
Mark
Abraham
Trigger correct
k
e
rnels under Cygwi
n
commit
|
commitdiff
|
tree
2011-10-27
Mark Ab
r
aham
Ma
d
e reading of bina
r
y
m
a
trice
s
mor
e
ro
b
ust
commit
|
commitdiff
|
tree
2011-10-19
Mark Abraham
Co
r
rected charge of CHARMM
zinc ion to +2
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Removed erroneous
use o
f
MASSV on BlueGene
commit
|
commitdiff
|
tree
2011-10-06
Mark A
b
raham
Fixes for GB k
e
rnel
commit
|
commitdiff
|
tree
2011-09-27
Mar
k
Abraham
Add
e
d tip f
o
r converting
.
xpm to something useful
commit
|
commitdiff
|
tree
2011-09-26
Mark Abraham
Dropp
e
d s
o
me hin
t
s
i
n
the documentation
commit
|
commitdiff
|
tree
2011-09-26
Mark Ab
r
aham
Removed CMake warning
f
o
r recent
OpenMPI versi
o
ns
commit
|
commitdiff
|
tree
2011-09-15
Mark
A
br
a
ham
Fix t
r
jconv -s
u
b
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
W
a
rning
a
bout trjconv -sub
n
eeding many files
open
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
g
_
s
h
am -mdata is an input fil
e
, not output file
commit
|
commitdiff
|
tree
2011-09-14
Mark Ab
r
aham
Fo
r
mat warning
b
e
t
t
er
commit
|
commitdiff
|
tree
2011-09-13
Mark A
b
raham
Fix pdb2gm
x
-d
e
bug
a
n
d
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mar
k
Ab
r
a
ham
F
ix for CMake finding L
A
PA
C
K
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Added ACE and
C
T3 to C
H
A
R
M
M27 aminoacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fixed charge
g
r
oups of CHARMM27 DNA/RNA
termi
n
al H
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fixes for CMa
k
e f
i
nding F
O
RTRAN library
n
ames
o
n POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark Ab
r
aham
Fix bug wit
h
large ints without
MPI_I
N
_
P
LACE
commit
|
commitdiff
|
tree
2011-09-01
Mark Ab
r
aham
M
a
de grompp note ab
o
ut non-zero charge more
u
seful
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraha
m
Re-imple
m
ented
g
e
n
e
r
a
t
ing default
p
r
otein inde
x
groups
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k Abraham
Adjuste
d
co
n
s
truction
o
f default
i
ndex groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abraham
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark A
b
ra
h
a
m
Fixe
d
g
_
disre dereferencing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
Ma
r
k Abr
a
h
a
m
Ex
p
lained terminal residues and A
M
BER in pdb
2
gmx -h
commit
|
commitdiff
|
tree
2011-08-16
Mark Abr
a
ham
Made free e
n
ergy
pertu
r
bation work w
i
th CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Abrah
a
m
F
i
xed
output bug i
n
demux
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abraha
m
Str
e
amlined smal
l
par
t
of pdb2gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark Abra
h
am
Read
i
ng a
.
g96 trajectory now caus
e
s fata
l
er
r
or
commit
|
commitdiff
|
tree
2011-07-11
Mark Abr
a
ham
Fix some iden
t
ifier naming issue
s
in last
commit
commit
|
commitdiff
|
tree
2011-07-11
Mark Abrah
a
m
Avoi
d
ed some inte
g
er overflows
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk Abraham
C
l
arified u
s
e of OPLS/AA zwitterion termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Fixe
d
improper
fil
e
clo
s
e with GB and mdrun -debug
commit
|
commitdiff
|
tree
2011-07-08
M
a
rk Abraham
Made
pdb2gm
x
e
r
r
or message less
cryptic
commit
|
commitdiff
|
tree
2011-06-29
Mar
k
A
b
r
aham
Rev
e
rt
"
draft"
commit
|
commitdiff
|
tree
2011-06-29
M
a
rk Abr
a
ham
Improved
e
rro
r
m
essage and docum
e
ntation
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
d
r
aft
commit
|
commitdiff
|
tree
2011-06-21
Mark Abraha
m
Expanded LINCS war
n
ing te
x
t
commit
|
commitdiff
|
tree
2011-06-07
Mar
k
Abraham
Fixed spell
i
ng of
reproducible
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Added referen
c
e to g_sa
s
-h
commit
|
commitdiff
|
tree
2011-05-11
Mar
k
A
b
raham
Cl
e
a
ned up g_sas help text
commit
|
commitdiff
|
tree
2011-05-09
Mar
k
A
braham
A
dded hint abo
u
t calling trjc
o
n
v more than onc
e
commit
|
commitdiff
|
tree
2011-05-09
Mark Abraham
Spaced out par
a
graphs in
t
rjconv he
l
p
commit
|
commitdiff
|
tree
2011-05-02
Ma
r
k
A
braham
Removed duplicate definition o
f
md_print_war
n
ing()
commit
|
commitdiff
|
tree
2011-05-01
Mark Abraham
Fixed
d
es
c
r
iption
o
f
.
mdp opti
o
n to
"
h-bo
n
d
s"
commit
|
commitdiff
|
tree
2011-04-14
Mark
Abraham
Removed unnec
e
ssary
#
i
ncludes
commit
|
commitdiff
|
tree
2011-04-14
M
ark
A
braham
Deleted d
u
plica
t
ed co
d
e
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Moved var
i
ous su
p
p
o
rt function
s
fo
r
do_md in
t
o m
d
lib
commit
|
commitdiff
|
tree
2011-04-14
Mark A
b
rah
a
m
Moved itera
t
ed-constr
a
ints
code into
mdlib
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k
A
braham
Moved heuristic
n
eighbor-l
i
st co
d
e
into mdl
i
b
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abraham
F
i
xed code duplication
commit
|
commitdiff
|
tree
2011-04-14
Mark Abra
h
a
m
Fixed header #
i
fnd
e
f
te
s
t
commit
|
commitdiff
|
tree
2011-03-30
Mark
Abraham
Removed us
e
less const
q
u
a
lifi
e
r
commit
|
commitdiff
|
tree
2011-03-30
Mar
k
A
braham
Suppressed
Cygwin C-o
n
l
y
compiler w
a
rnings
commit
|
commitdiff
|
tree
2011-03-26
Ma
r
k A
b
raham
Fixed g_cluster l
o
gi
c
error
commit
|
commitdiff
|
tree
2011-03-26
Mark A
b
raham
Mad
e
gmx_r
m
pbc_t ob
j
ec
t
functions not
s
e
gfa
u
lt
commit
|
commitdiff
|
tree
2011-03-26
Mark Abrah
a
m
F
ixed mat
i
o
.
c sf
r
ee() that made Dv
d
S cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abraham
Added grompp note
a
bout avoiding zero
-
step EM
commit
|
commitdiff
|
tree
2011-02-16
Mar
k
Abra
h
am
Clarified source of g_rmsf refer
e
nce frame
commit
|
commitdiff
|
tree
2011-02-13
Ma
r
k Ab
r
ah
a
m
Added work
a
r
ound for F_GB
1
3 duplicates
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraha
m
F
i
xed e
r
ron
e
ou
s
floating-
p
oint comparison
commit
|
commitdiff
|
tree
2011-02-12
Mark Abraham
A
dded note
a
b
ou
t
doing
r
ep
e
at
i
nvocations
of genbox
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Removed ancient CVS
tag
l
i
nes
commit
|
commitdiff
|
tree
2011-02-11
Mark A
b
r
aham
U
s
e
d some spacing to m
a
ke
c
od
e
readable
commit
|
commitdiff
|
tree
2011-02-11
M
a
rk Abraham
Used
s
ymboli
c
constant more consistentl
y
commit
|
commitdiff
|
tree
2011-02-11
Mark Abraham
Made the "multiple
s
e
t
tles"
f
atal
error
more h
e
l
p
ful
commit
|
commitdiff
|
tree
2011-02-02
M
a
rk Abraham
Fixed minor i
s
sue with
r
eplica exchange
commit
|
commitdiff
|
tree
2011-01-28
Mark Abraham
Added
f
orgotten f
i
l
e
commit
|
commitdiff
|
tree
2011-01-28
Mark Ab
r
aham
Turned
g
_options
i
n
t
o
a normal GROMACS tool
commit
|
commitdiff
|
tree
2011-01-28
M
a
rk
A
braham
Renam
e
d src/tools/o
p
tions
.
c
commit
|
commitdiff
|
tree
2011-01-28
Mark
A
braha
m
Improved grom
p
p docum
e
nta
t
io
n
commit
|
commitdiff
|
tree
2011-01-25
Mar
k
A
braha
m
Improved geni
o
n -h
commit
|
commitdiff
|
tree
2011-01-25
Mar
k
A
b
ra
h
am
Relocated so
m
e
t_matrix document
a
t
ion
commit
|
commitdiff
|
tree
2011-01-25
Mark A
b
raham
Improved do_dssp
-ssdump output
commit
|
commitdiff
|
tree
2011-01-25
Mark Abra
h
a
m
Impro
v
ed do
_
dssp
-
sc ou
t
put
commit
|
commitdiff
|
tree
2011-01-23
Mar
k
Ab
r
aham
Remove g_highway fr
o
m list of programs
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Improved c
o
nversion
o
f documenta
t
i
on to LaT
e
X
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
Improv
e
d consistenc
y
of text style usage
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
braham
Minor wording fi
x
e
s
commit
|
commitdiff
|
tree
2011-01-23
Mark
A
braham
M
oved
o
ptions
.
c to tools subdir
commit
|
commitdiff
|
tree
2011-01-23
Mark Abraham
cmake: ad
d
ed b
a
c
k
gsl
support (GMX_GSL, disa
b
l
ed by
.
.
.
commit
|
commitdiff
|
tree
2011-01-23
Ch
r
i
s
toph Jungha
n
s
cmake:
a
d
ded GMX
_
XML
t
o fully disable xml su
p
port
commit
|
commitdiff
|
tree
2011-01-23
Chri
s
toph Ju
n
ghans
cmake: add support for e
x
ter
n
al bl
a
s/
l
apack
commit
|
commitdiff
|
tree
2011-01-20
Mark Abraham
Added NHE to OPLS/AA pdb2gmx hydrog
e
n d
a
ta
b
ase
commit
|
commitdiff
|
tree
2011-01-20
Mark A
b
ra
h
am
Made gmxdu
m
p error m
e
ssage
cl
e
arer
.
commit
|
commitdiff
|
tree
2011-01-18
Mark Abraham
Improved
.
md
p
file comment about the 'define' f
i
eld
commit
|
commitdiff
|
tree
2011-01-17
Ma
r
k Abraham
Fix An
g
s
trom <=> nm error in do
c
umentati
o
n
commit
|
commitdiff
|
tree
2011-01-13
Mark
A
br
a
ham
Made src/k
e
rnel/repl_ex
.
c l
e
gible
commit
|
commitdiff
|
tree
2011-01-07
Mark Abraham
Added
n
ote th
a
t
g_msd
-
mol does tre
a
t PBC (by
makin
g
.
.
.
commit
|
commitdiff
|
tree
2011-01-07
Mar
k
Abraham
Implemen
t
ed effecti
v
e test for MP
I
_IN
_
PLACE, th
a
nk
s
.
.
.
commit
|
commitdiff
|
tree
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