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Added 1 analysis tool manual.
2011-04-04
David
van
d
er Spoel
A
d
ded 1 analysis tool man
u
al
.
commit
|
commitdiff
|
tree
2011-04-04
David
v
an der Spoel
Merge
branch 'release-4-5-patches'
i
nto orderparm
commit
|
commitdiff
|
tree
2011-04-04
Dav
i
d
v
a
n
der
S
poel
L
ate
s
t
fixe
s
fro
m
Bjorn S
t
een Saethre
commit
|
commitdiff
|
tree
2011-03-24
David va
n
der Spoel
Added
Bjorn's
c
ode,
i
mplemented running aver
a
ge
f
iltering
.
commit
|
commitdiff
|
tree
2011-03-05
Dav
i
d van d
e
r S
p
oel
Merge branch 'release-4-5-p
a
tches' of
g
it@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David van der Spoel
Fixed SEGV in eneconv when using the
-
e flag
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
van der
S
poel
Fixed more PBC and index
i
ng stuff
.
commit
|
commitdiff
|
tree
2011-01-30
Davi
d
van der S
p
oel
Fixed
t
ypo
.
commit
|
commitdiff
|
tree
2011-01-30
David van der
Spoel
Me
r
ge br
a
nch
'release-4-5-
p
atches'
i
nto
o
r
derpa
r
m
commit
|
commitdiff
|
tree
2011-01-29
David v
a
n der Spoe
l
Merge
b
ran
c
h
'releas
e
-4
-
5-patches' of git@git
.
g
r
o
macs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
D
avid van
d
er Spoel
Added
code in g
_
nmeig to compute the quantu
m
cor
r
e
c
ti
o
ns
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David van der Sp
o
e
l
Merge b
r
an
c
h 'release-4-5-pa
t
ches' of
g
it@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
Dav
i
d van der Spoel
Fixe
d
bug 678 whi
c
h was du
e
t
o
calling gmx_fatal without
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
D
avid van der Spoel
Merge b
r
a
n
c
h
'release-4-5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van de
r
Spoel
Added warning in g_dipole
s
commit
|
commitdiff
|
tree
2010-12-23
David van
d
er Spo
e
l
Fixed bug in
statist
i
cs which did not allow fitting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
a
vid va
n
der Spoe
l
Me
r
ge branch 'release-4-
5
-
p
atches'
o
f git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Davi
d
van
der Spoel
Added
1 quote
.
commit
|
commitdiff
|
tree
2010-12-09
David van der Spoel
Add
e
d fatal e
r
ror
f
or whe
n
people use
ene
r
gy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
David
v
an der Spoel
Fixed bugzilla 616 a
b
o
ut formatting in
t
he help text
.
commit
|
commitdiff
|
tree
2010-11-26
David van der Sp
o
el
Fi
x
e
d SEGV
b
ug in g_
s
ham
.
commit
|
commitdiff
|
tree
2010-11-18
Da
v
id v
a
n der Spoel
Made
prin
t
ing in chec
k
_multi_init
c
on
d
itiona
l
, depending
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
David van der
Spoel
Fixed bug 608 by
t
hrow
i
ng a fatal error in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
D
a
v
id va
n
der Spoel
Merge b
r
anch 'release-4-5-
p
atc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David
v
a
n de
r
S
p
oel
Merge
b
ranch
'releas
e
-4-5-patc
h
es' of git
.
g
ro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David v
a
n
der Spoe
l
Fixed
c
o
mpi
l
ation
i
ssues with C99 compati
b
ili
t
y
.
commit
|
commitdiff
|
tree
2010-10-07
David va
n
der Spoel
Fixes an
d
s
m
all a
d
ditio
n
s to g_wham
,
due
t
o
Jochen
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David van der Spoel
Re-added g_
k
inetics
t
o src/tools/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
Da
v
i
d van der Spoel
Added softwa
r
e
-
r
el
a
t
e
d quote
commit
|
commitdiff
|
tree
2010-09-24
David va
n
d
e
r Sp
o
el
Updated to reflect bug 557
.
commit
|
commitdiff
|
tree
2010-09-20
David van der Sp
o
el
Merge branch
'
r
elease-4-5-pat
c
h
es' of git
@
gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
D
a
vid van der Spoel
Fi
x
ed bug h
t
tp://bugzilla
.
g
romacs
.
org/sho
w
_bu
g
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-16
Davi
d
van der Spoel
Corrected n
a
me
o
f
one o
f
t
h
e develo
p
e
r
s list
e
d
i
n he
a
der
.
commit
|
commitdiff
|
tree
2010-09-14
D
a
v
id van der Spoe
l
Fixed bug
553 b
y
checking
w
het
h
er an atom name is lo
n
ger
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David van
d
er
Spoel
F
i
xed dem
o
to work with
n
ew pdb2g
m
x
that requires two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
D
avid van der S
p
oel
Made genrestr -constr to pro
d
uce con
s
train
t
s
of t
y
pe
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David v
a
n d
e
r Spoel
Fixed
b
ug 417
.
commit
|
commitdiff
|
tree
2010-08-19
David
van der
S
p
oel
Fixes more mise
r
y in fu
n
ction ski
p
str, w
h
ere poi
n
ters
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Da
v
id van de
r
Spoel
Added two m
i
ssing include
files
.
Fixed ho
r
rible co
d
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Da
v
id van der
Spoel
Fi
x
ed reuse of varia
b
le as tem
p
varia
b
l
e
b
efore pr
i
nting
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David van der Spoel
F
i
xed
bug 487 acco
r
d
i
ng to provid
e
d
p
atch
.
commit
|
commitdiff
|
tree
2010-08-03
David v
a
n
der
Spo
e
l
Fixed
documentation text
a
cco
r
ding to bugzilla 486
commit
|
commitdiff
|
tree
2010-08-01
Davi
d
van der Spoel
Merge branch '
r
elease-4-5-patches
'
o
f
git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Da
v
id van der Spoel
Moved pdb2top
.
h
f
rom src/ke
r
nel to
i
nc
l
ud
e
t
o
allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David van der
Spoe
l
Renamed typename to my_ty
p
ename in i
n
dex
.
c
sin
c
e
typen
a
me
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
David van d
e
r Spo
e
l
Fixed compila
t
ion issue
corre
s
p
o
nding
t
o bu
g
468
commit
|
commitdiff
|
tree
2010-07-14
D
avid van der Spoel
Fixed bug 4
6
7
r
e
alting to pdb2gmx output of the w
a
ter
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David v
a
n
d
e
r Spoel
Added citation for scattering f
a
cto
r
s
.
Use
d
in g
_
rd
f
.
.
.
commit
|
commitdiff
|
tree
2010-07-14
David van der Spoel
Added more at
o
m
s
to the sc
a
t
t
ering factor
dat
a
file
.
commit
|
commitdiff
|
tree
2010-07-14
David
v
an der Spo
e
l
Fixed bug
462
.
p
db2
g
mx shoul
d
now
p
roduce th
e
correct
.
.
.
commit
|
commitdiff
|
tree
2010-07-13
Dav
i
d va
n
d
er Spoel
Fixed bug
4
6
6 by commenting
ou
t
the
o
f
f
ending
lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-12
David van der Spoel
M
erge
branc
h
'master
'
of git@gi
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-12
Dav
i
d
v
an d
e
r Spo
e
l
Added initializa
t
ion of pbc str
u
ct in g
e
nborn
.
c
.
commit
|
commitdiff
|
tree
2010-07-09
David van
d
er Spoel
Adde
d
i
nitialization of
pbc structure b
e
f
o
re calc_gb_forces
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
D
a
vid v
a
n
d
er Spoel
Merge branch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-08
Da
v
id van
der
S
p
oel
Added bon
d
e
d
typ
e
s
section to rtp files
.
It might
be
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van
d
e
r S
p
oel
Removed p
o
s
s
ible SEGVs in rmpbc in case ePBC = No
.
commit
|
commitdiff
|
tree
2010-07-08
Davi
d
van der Spo
e
l
Merge br
a
nch '
m
ast
e
r' of
git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-07
David
v
an
d
er
S
poel
Merge br
a
nch 'master' of gi
t
.
gromac
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-07
D
avid van
d
er
Spoel
Fix
e
d miserable b
u
g
in commrec
.
h where an int array
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
D
a
vid van
der Sp
o
el
Fixed bug in gmx_sumf_co
m
m
w
here a double arr
a
y
was
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
David van der Spo
e
l
Merge br
a
nch
'
master' of git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-05
David van der
S
p
o
e
l
Merge branch 'master' of
g
it
.
gr
o
macs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-05
Dav
i
d van
d
e
r
S
poel
Added sfa
c
t
o
r
.
dat to the insta
l
lation ta
r
ge
t
s i
n
s
hare
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
Dav
i
d van der
S
poel
Fixed include statements su
c
h that dou
b
le precisi
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Davi
d
v
a
n der Sp
o
el
Mer
g
e branch 'master' of g
i
t
.
groma
c
s
.
o
r
g:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-02
David van der S
p
oel
M
a
d
e removi
n
g pbc n
o
n-static
.
This affects many
a
nalysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Da
v
id van d
e
r Sp
o
e
l
Merge bran
c
h 'm
a
st
e
r
' of git
.
gromac
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-02
D
avid va
n
d
er
S
p
o
el
Fixed bug h
t
tp
:
//bugzilla
.
gr
o
mac
s
.
o
r
g/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
D
avid van der Spoel
Fi
x
ed http://bugzilla
.
gromacs
.
org/show_bug
.
c
gi
?
id=457
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David v
a
n der Spoel
Me
r
ge branch 'master' of git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-06-30
David van
der
Spoel
F
i
xed bug
i
n
b-factors ou
t
p
u
t by g_confrms
.
T
he
y
wer
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Dav
i
d va
n
de
r
Spoe
l
Ad
d
ed missing argum
e
n
t
step to tr
o
tt
e
r_updat
e
.
H
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David
v
an de
r
Spoe
l
Merge branch
'
m
aster
'
of git
.
gromacs
.
org:
g
romac
s
commit
|
commitdiff
|
tree
2010-06-27
David van
der Spoel
Updated C
M
akeLis
t
s
.
txt i
n
n
gmx dire
c
tory to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der
S
poel
Fixe
d
many issues regarding t
o
compilati
o
n wit
h
C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David va
n
der
S
poel
Fixed Make
f
i
le
.
am leading to w
a
rnings
.
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van de
r
Spoel
Fix
e
d make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
D
a
vid v
a
n
d
er Sp
o
e
l
Merge branch
'm
a
ster' of git
.
g
r
o
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-14
David van
d
er S
p
o
e
l
Added m
o
re fixes in comment te
x
ts, ge
n
erously pr
o
vided
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Dav
i
d van d
e
r Spoel
Fi
x
ed a lot of sp
e
lling errors
in comments and docu
m
e
ntation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
Da
v
id van de
r
Spoel
Merge branch
'
mas
t
er' of git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-11
Dav
i
d van der
S
poel
Fixed force field files for ATP
in order to clear bug
commit
|
commitdiff
|
tree
2010-06-10
D
avid
v
an der Spoel
Merg
e
branch 'm
a
st
e
r' of
g
it
.
gromac
s
.
or
g
:groma
c
s
commit
|
commitdiff
|
tree
2010-06-10
David van
der
S
poel
Made
le
g
end more o
r
less wo
r
k in g_chi
.
D
on't know
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
F
ixed SEGV in g_
c
hi
a
s des
c
ribed
i
n
bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spo
e
l
Added
option -nopbc t
o
g
_
r
msdist in orde
r
to fix
commit
|
commitdiff
|
tree
2010-06-10
David van der
S
poel
Pedan
t
ic change
i
n
the check whether a f
i
lename i
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d van der Spoel
Renamed some
p
rograms to foll
o
w the g_ do
c
trine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoe
l
C
leaned up and
r
enamed file
s
in
n
g
mx d
i
rectory to better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoe
l
Rename
d
some files
i
n a ro
u
n
d
abo
u
t way to
ad
h
ere to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
D
avid van der Spoel
Removed average
.
c
,
that functiona
l
i
t
y
is now in g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Fixed
strange typo
in g
m
x_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
D
a
v
i
d
v
an der Spoel
Moved warning mes
s
age
in a
d
d_atom
t
y
p
e to
b
e printed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David van der Spo
e
l
Made x2to
p
(ve
r
y)
s
lightly functional again
.
S
t
ill
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spoel
Changed error messa
g
e for se
t
tl
e
problems, s
u
ch that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d van der Spoel
Add
e
d ex
p
l
icit angle in A
C
E declaration i
n
g
roma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van d
e
r Spoel
Fixed typ
e
in gmx_morph
.
c
: efTRO -
>
e
f
TRX which lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
d
er Spo
e
l
Fixe
d
bug 396
.
In f
a
ct i
t
was already
f
i
xed
partly
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id van der Spoel
Fixed bug
4
01 by implementing the proposed patch that
.
.
.
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|
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|
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