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New analysis tool to compute the free volume and total volume.
2013-06-14
Dav
i
d van der
S
poel
Ne
w
analysis tool to co
m
p
ute t
h
e fr
e
e volum
e
and
total
.
.
.
commit
|
commitdiff
|
tree
2013-05-16
David
van der Spoel
F
ixed
two compilation issues
.
commit
|
commitdiff
|
tree
2013-05-02
D
a
vid
v
an der Spoe
l
Fixes #1238 g_hydorder does not
c
all s
e
t_pbc
.
commit
|
commitdiff
|
tree
2013-05-01
David van der Spoel
Mer
g
e "Updated
s
o
u
rce for Van der Waal
s
radii
.
"
commit
|
commitdiff
|
tree
2013-04-25
David van der Spoel
Updated
s
ource
f
or V
a
n der Waal
s
radii
.
commit
|
commitdiff
|
tree
2013-04-16
D
a
vid
v
an der Spoel
Merge "
c
orrected gro
m
pp rvdw charge-gr
o
up radii
check
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David va
n
d
e
r
Spoel
Merge "
a
dded mdrun
c
heck for Verle
t
+perturbed a
t
oms
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
David van der Spoel
Merge "Ad
d
histogram output for 'gmx gangle'
.
"
commit
|
commitdiff
|
tree
2013-03-07
Dav
i
d
van der Spoel
Fixes #1183 P
B
C bug in g_mindi
s
t
commit
|
commitdiff
|
tree
2013-02-15
D
a
v
id van der S
p
oel
Merge
"Fixed an
initialization
i
ssue in
gmx_dip
o
les
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
D
a
vid
van der S
p
oel
Pla
i
n
text quotes
.
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
Merg
e
"Fixing trjconv -sub" into release-
4
-5
-
p
a
tches
commit
|
commitdiff
|
tree
2013-01-14
David v
a
n
d
e
r Spoel
Me
r
ge "Noting that
and why gmxd
u
mp -s -sys is broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
David va
n
der
S
poel
Fixes
#
994 confusion in atomprop
.
commit
|
commitdiff
|
tree
2013-01-07
Da
v
id van
d
er
S
poe
l
M
e
r
g
e
"Re
m
o
v
e
d
reference
t
o
n
one
x
istent file in g_helix
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
David va
n
der
S
poe
l
Merge "Merge rele
a
se-4-5-patches into release-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
D
a
vid van der Spoel
Fixes #1
0
35 NaN i
n
g
_cluster ou
t
p
u
t
.
commit
|
commitdiff
|
tree
2012-11-20
David van der Spoel
Fixes
bug
i
n g_hbon
d
tha
t
makes it produce fatal er
r
o
r
.
commit
|
commitdiff
|
tree
2012-11-17
David
v
an der Spoel
Merge "Added grompp warning" into release-4-6
commit
|
commitdiff
|
tree
2012-11-17
David van
d
e
r S
p
oel
Merge "Remo
v
e rest
o
f th
e
xml support" in
t
o
release-4-6
commit
|
commitdiff
|
tree
2012-11-16
David v
a
n der Sp
o
el
Merge
"
Removes unu
s
ed files"
into release-4-6
commit
|
commitdiff
|
tree
2012-11-12
David van
d
e
r
S
p
oel
F
ixes #
1
020 options in g_enemat
commit
|
commitdiff
|
tree
2012-10-26
D
a
vid
v
an der
S
p
oel
M
e
rge "F
i
xe
d
Pul
p
Fiction quote" into rele
a
se-4-5-patc
h
es
commit
|
commitdiff
|
tree
2012-10-21
Dav
i
d van
d
e
r Spoel
Fix
e
d
Bug #593
a
bout memo
r
y hole i
n
trjc
a
t
.
commit
|
commitdiff
|
tree
2012-10-13
David van der Spoel
Merg
e
"
F
i
x
ing
is
s
ues with replica
exchange" into release-4-6
commit
|
commitdiff
|
tree
2012-10-12
Dav
i
d van der Spoel
Mer
g
e "[to
o
ls] g_sans - add trajectory avereging"
commit
|
commitdiff
|
tree
2012-10-04
David van der Spoel
Set
ret
u
r
n
value to FALSE (0) in
e
stimate_dt in l
i
bxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-15
David van d
e
r S
p
o
e
l
Me
r
ge "Adapted NMR rel
a
ted dat
a
to new pdb f
o
rmat
.
.
.
.
commit
|
commitdiff
|
tree
2012-09-07
David van der Sp
o
el
Adapted
N
MR re
l
ated d
a
ta to new pdb
format
.
commit
|
commitdiff
|
tree
2012-09-04
David van der Sp
o
el
Made tu
t
o
r
ial slightly
less
c
on
f
using
.
commit
|
commitdiff
|
tree
2012-08-16
D
a
vid van der Spoel
Optional computation of fluct
.
props in
g_e
n
ergy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-07-15
Dav
i
d van
der Spoel
M
e
rge "Autogenerate gromacs
.
7 from
p
rograms
.
tx
t
" into
.
.
.
commit
|
commitdiff
|
tree
2012-07-05
David v
a
n der Spo
e
l
Merge "Improve Pr
o
gramInfo and use
it
e
v
e
rywhere
.
"
commit
|
commitdiff
|
tree
2012-06-30
D
avid v
a
n der
Spoel
Fixed bug in free ene
r
gy cal
c
ulatio
n
for
M
orse poten
t
ia
l
s
commit
|
commitdiff
|
tree
2012-06-21
David van d
e
r Spoel
Fixes #96
1
- Shake rep
o
rts
wrong err
o
r
commit
|
commitdiff
|
tree
2012-06-16
D
avid van
der Spoel
Fixes
#
882 - looping bug in trxio
.
c
commit
|
commitdiff
|
tree
2012-05-27
David van der Spoel
Merge "added expl
i
cit sqrtf to
the f
l
o
a
t
v
e
r
s
i
o
n of
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
Dav
i
d van der Spoe
l
M
erge
"grompp
n
o
w
retains the or
d
e
r
of bonds converted
.
.
.
commit
|
commitdiff
|
tree
2012-05-03
David
van der Spo
e
l
Mer
g
e
"
R
e
moved u
n
used code
from sr
c
/
kernel/
.
"
commit
|
commitdiff
|
tree
2012-04-29
David van der Spoe
l
Mer
g
e "changed n
u
mber of
i
atoms for F_SETTLE
f
r
om 1
.
.
.
commit
|
commitdiff
|
tree
2012-04-29
David van
d
er
Spoe
l
Merge "added support for graphs
n
o
t
starting at 0"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
David van der Spoel
Mer
g
e "[tools]
g
_sans
- splite
d
out fixes and added
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Davi
d
van der Spoel
Merge "Various i
m
provements to shell
c
ode" into rele
a
se
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
Davi
d
van der Spoel
Me
r
ge "Added
support for
d
ssp2
.
X with t
h
e -ver o
p
tion
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
D
a
v
i
d
van
d
er Spoel
Merge "Expanded the help
t
e
x
t
regarding
t
h
e -r2 and
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
David van
der
Spoel
M
erge "Improved pdb2gmx error messag
e
" into r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
David
van der Spoe
l
Merge "
F
ix typo in Cl
a
ng CFla
g
s"
i
n
to rel
e
ase-4-5-p
a
tch
e
s
commit
|
commitdiff
|
tree
2012-03-18
David van de
r
Spoel
Mer
g
e "Merge release-
4
-5-patches into release-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-03-17
David v
a
n
der Spoel
Removed
qhop fil
e
s from this branch
.
commit
|
commitdiff
|
tree
2012-03-10
D
a
vid van der Spoe
l
Vibration spectra from velocity ACF
or Normal modes
.
commit
|
commitdiff
|
tree
2012-03-09
Davi
d
van der Spoel
Merge "Improved cryptic
err
o
r message" into
r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
David van der Spoel
Merg
e
"Minima
l
support
for
C
lan
g
" into release-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
David van de
r
Spo
e
l
M
erge "
M
i
n
o
r f
o
rmatt
i
ng f
i
xes to
.
mdp option documentation
.
.
.
commit
|
commitdiff
|
tree
2012-02-03
David van der Spoel
Mer
g
e
"Improved
t
he accuracy of t
h
e sd1 integrator
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
Merge "
g
_
s
ans -
tool to c
o
mpute
SANS spe
c
t
ra" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
D
a
vid van der Spoel
Merge "
F
i
x
ed error mes
s
age to identify the correct
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
Davi
d
van der Spoel
M
e
rge
"
F
ixed trjc
o
nv -sub" int
o
r
e
lease-4-5-patc
h
es
commit
|
commitdiff
|
tree
2012-02-01
David van der S
p
oel
Merge
"
Improved error message" into rele
a
se-4-5-
p
a
t
ches
commit
|
commitdiff
|
tree
2012-01-31
Da
v
id van der Spoel
Merg
e
"Fix ICC on
Wi
n
dows Build" in
t
o rele
a
se-4-5
-
patc
h
e
s
commit
|
commitdiff
|
tree
2012-01-31
D
avid van der Spoel
Changed order of parameters in top fil
e
commit
|
commitdiff
|
tree
2012-01-25
Dav
i
d
v
an der Spoel
Added two new bonded function
s
.
commit
|
commitdiff
|
tree
2012-01-22
David van der
Spoel
Merge "Print context on reference data
c
he
c
k f
a
ilure
.
"
commit
|
commitdiff
|
tree
2012-01-20
D
a
vid van der Spoel
Merge "Fixed timing m
e
asurem
e
nts
.
" into release-
4
-5
.
.
.
commit
|
commitdiff
|
tree
2012-01-17
David van der Spoel
Repla
c
e std
e
rr by stdou
t
in e
d
i
t
c
onf
termina
l
output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David van
d
er
S
poel
I
nt
r
oduced
fa
t
al error
in grom
p
p
for incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-10-18
David
v
an der Spoel
M
erge "Doxygen u
p
d
a
tes for
fatalerror
m
o
d
u
l
e
.
"
commit
|
commitdiff
|
tree
2011-10-18
Dav
i
d van der Sp
o
el
Me
r
ge "Mi
s
c
.
Doxygen impr
o
vements
.
"
commit
|
commitdiff
|
tree
2011-09-21
Davi
d
van
d
e
r Spoel
Commented out part
of
t
hi
s
new pro
g
ram
t
h
at was not
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van d
e
r S
p
oel
Fixe
d
do
c
um
e
n
tation
i
ssue described in redmine is
s
ue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der S
p
oel
Fixed d
o
cumentation issue
described in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
D
avid
van der
S
poel
Fixed compil
a
t
i
on i
s
sues
commit
|
commitdiff
|
tree
2011-09-19
David van
der Spoel
Res
o
lved gerrit
i
ssue h
t
tps://gerrit
.
gromacs
.
org/#cha
n
ge,126
commit
|
commitdiff
|
tree
2011-09-13
David va
n
der S
p
o
e
l
Added warn
i
ng
l
i
ne
.
commit
|
commitdiff
|
tree
2011-07-20
D
av
i
d van de
r
Spoel
Merge branch 'r
e
lease-4-5-patches' of gi
t
@g
i
t
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
David van
d
er Spoe
l
Ad
d
ed
i
nitial
i
zatio
n
of ar
r
a
y
s a
f
ter s
r
e
n
e
w
call
.
commit
|
commitdiff
|
tree
2011-07-20
Da
v
id van d
e
r Spoel
A
d
d
e
d initialization
o
f arrays after
s
r
en
e
w call
.
commit
|
commitdiff
|
tree
2011-07-02
Da
v
id van
der S
p
o
el
M
erge branch 'ma
s
ter
'
of git@git
.
g
r
oma
c
s
.
org:
g
ro
m
acs
commit
|
commitdiff
|
tree
2011-07-02
David
v
an der Spoel
Compilation fixes in gm
x
_densi
t
y
.
c and histogram
.
c
p
p
commit
|
commitdiff
|
tree
2011-07-01
David van der Spoel
M
e
rge
b
ranch 'release-4-5-patche
s
'
of git@git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der
S
poel
Me
r
ge branch 'r
e
lease
-
4
-5-pa
t
ches' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der Spoel
Added g_dos
target
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van
d
er Spoel
Fur
t
her patch
e
s to f
l
uc
t
uation code and density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Add
e
d computation of A a
n
d U
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Upd
a
t
e
d
, made default tole
r
ance for bisector mor
e
stringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David
v
an der Sp
o
e
l
Fixed
w
eight functions an
d
adde
d
-dump option (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid va
n
d
er Spoel
U
p
da
t
ed
.
Fixed computat
i
on of frequenc
y
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Sp
o
el
Up
d
ated the eqn for
c
o
m
p
u
ti
n
g Delta
.
Now g
e
t rough
l
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Sp
o
el
Mul
t
iplied the DoS by th
e
t
im
e
step (b
e
tween frames)
.
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spo
e
l
U
pdated
.
Now com
p
utes diffusion
f
ro
m
the VACF
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id va
n
der
S
poel
Fixed
x
-axis to be
in reciprocal cm
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
v
an der Sp
o
el
Fur
t
her update
s
.
Stil
l
not
pe
r
fect
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
S
p
oel
Added stuff t
o
compute cP and
S
.
Not
complet
e
yet
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Upd
a
ted to compute
t
he flu
i
d
ic
i
ty
.
Added refs for citation
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Updated
commit
|
commitdiff
|
tree
2011-05-31
David van d
e
r Spoel
Ne
w
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Further
patch
e
s to fluctuation code a
n
d
d
ensity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David v
a
n der Spoel
Merg
e
b
ra
n
ch
'
mas
t
er
'
of g
i
t@gi
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id
v
an de
r
Spoel
Ad
d
ed quote
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Further patches
t
o fl
u
ctuation
c
ode
an
d
density of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id
van der Spoel
Added quo
t
e
.
commit
|
commitdiff
|
tree
next