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MSD tests for the -mol option.
2015-09-10
David van der Sp
o
el
Moved conten
t
fro
m
mdrun
.
h
t
o separate
h
eaders
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Rem
o
ved <sys/types
.
h> and "types/constr
.
h" from t
y
pedefs
commit
|
commitdiff
|
tree
2015-09-09
Davi
d
va
n
d
er
Spoel
Removed fileio/trx
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
va
n
der S
p
oel
Mo
v
ed
functions operat
i
ng on force
r
e
c
to s
e
parate
h
eader
.
commit
|
commitdiff
|
tree
2015-08-28
David van de
r
Spoel
Added energ
y
(edr) file type to
Options
h
eaders
.
commit
|
commitdiff
|
tree
2015-08-28
David van d
e
r Spo
e
l
Ad
d
ed
addit
i
onal c
o
n
s
tructor t
o
StringStream clas
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
D
a
vid van
der Spo
e
l
Made
o
utput from dumpi
n
g
nei
g
htborlists easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
Davi
d
van der Spoe
l
Chan
g
e initial
par
a
met
e
rs
for testing expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David
v
an der Spoe
l
C
o
de for c
h
ecking xvg
f
i
l
es in testutils
.
commit
|
commitdiff
|
tree
2015-04-17
Dav
i
d van der S
p
oel
Updated
exponential fitting
t
o make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David v
a
n der
S
poel
Clarifie
d
comments fo
r
time-dependent e
l
ectric
f
ields
.
commit
|
commitdiff
|
tree
2015-04-08
David v
a
n der Spoel
F
i
xed incorrect output of gb_algori
t
h
a
s
sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der
S
poel
Up
d
ated docu
m
entation f
o
r electric fie
l
ds
.
commit
|
commitdiff
|
tree
2014-12-13
David
v
an
der Spoel
Four
n
ew
quotes from around the world
.
commit
|
commitdiff
|
tree
2014-11-28
David van der Spoel
Fixes r
e
cen
t
l
y
int
r
odu
c
e
d
b
ug in gmx ana
l
yz
e
.
commit
|
commitdiff
|
tree
2014-11-24
David
v
an
d
er
Spoel
Added warn
i
ngs for ewal
d
-geometry a
n
d surface-epsilon
commit
|
commitdiff
|
tree
2014-10-28
David va
n
d
e
r
Spoel
E
ven m
o
re refreshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David
v
a
n d
e
r Spoel
Reorganizin
g
analysis of correlation funct
i
ons
.
commit
|
commitdiff
|
tree
2014-09-23
David
v
an der Spo
e
l
Fix
e
s poten
t
ial bug i
n
neighborsear
c
hing
.
commit
|
commitdiff
|
tree
2014-09-17
D
a
vid van der Spoel
M
e
rge release-5-0 in
t
o master
commit
|
commitdiff
|
tree
2014-09-10
David v
a
n der Spoel
Remove
.
t
p
a,
.
tpb,
.
tpx,
.
tr
j
files
.
Part
of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
David v
a
n der
Spoel
Fixes
issue with vsiten
a
nd verlet buffe
r
s
.
commit
|
commitdiff
|
tree
2014-07-05
David van der Sp
o
el
Fix
e
d
inconsis
t
ency in blocka handlin
g
.
commit
|
commitdiff
|
tree
2014-06-29
David van der Spoel
Fi
x
e
s #1532, SEGV
in g_cu
r
r
e
nt
.
commit
|
commitdiff
|
tree
2014-06-25
Da
v
i
d
va
n
der Spoel
Added check for
d
omain decompo
s
ition and shells
.
commit
|
commitdiff
|
tree
2014-06-24
David van der Spoel
Added check in
g
rompp for shells
an
d
inputrec
issue
s
.
commit
|
commitdiff
|
tree
2014-06-22
David van der Spoel
Impl
e
me
n
ted fat
a
l er
r
or for nstcalcen
e
r
g
y!=
1
with
shells
.
commit
|
commitdiff
|
tree
2014-06-13
David van d
e
r
S
poel
Fix m
e
mo
r
y-us
a
ge error in g_chi
commit
|
commitdiff
|
tree
2014-06-11
D
a
v
i
d van der Sp
o
el
Fix
e
s
bug
w
here -e an
d
-dt flags did n
o
t work any
m
ore
.
commit
|
commitdiff
|
tree
2014-06-07
D
a
vid van der Spoel
Merge "Merge re
l
ease-5-0 into m
a
ster"
commit
|
commitdiff
|
tree
2014-06-07
David van der Spoel
Merge release-5-0 in
t
o m
a
ster
commit
|
commitdiff
|
tree
2014-06-02
Da
v
id van der Spoel
Fixed
w
rong journal ref
e
rence in manu
a
l
commit
|
commitdiff
|
tree
2014-05-31
David van der Spoel
Permit trjconv to read and
w
rite vel
o
c
i
t
ies
w
it
h
TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
D
a
vid van der S
p
oel
F
ixes a compl
i
cated bug in g_a
n
aei
g
.
commit
|
commitdiff
|
tree
2014-05-15
David va
n
der
Spoel
Added cmake
p
rofiling support
commit
|
commitdiff
|
tree
2014-04-02
David van der
S
poel
Removed possib
i
lit
y
o
f
c
om
p
iling with
G
SL
.
commit
|
commitdiff
|
tree
2014-03-31
David
van der Spoel
Fixed compi
l
a
t
ion issue in fg
r
id
.
cpp due to int/en
u
m
commit
|
commitdiff
|
tree
2014-03-06
D
a
vid
va
n
der Spoel
Six new q
u
otes from cl
a
ssic l
i
terature
.
commit
|
commitdiff
|
tree
2014-02-11
David van der
Sp
o
el
Fixe
d
a
n
other
v
mdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
David van der Spoel
Move
d
cond
i
tional
c
m
ake
c
ode
f
o
r
vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
David van
der Spoel
Moved
ran
d
om num
b
er gen
e
rator code to
sepa
r
ate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David van der Spoel
Thi
s
p
a
t
c
h moves
the s
t
atistics library to its o
w
n
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David
v
a
n der Spoel
This pat
c
h moves prep
r
o
c
e
ssing he
a
ders
t
o
g
mx
p
re
p
rocess
commit
|
commitdiff
|
tree
2014-01-15
D
avid van der Spo
e
l
This patch
m
oves the
nrama
.
[ch]
t
o
t
he gmxana dir
.
commit
|
commitdiff
|
tree
2014-01-13
David van der Spoel
C
l
ea
n
ed up list of GROMACS author
s
commit
|
commitdiff
|
tree
2014-01-09
David van der Spoel
Fixed p
r
ecisio
n
in ther
m
al e
x
pansion coefficien
t
cal
c
.
commit
|
commitdiff
|
tree
2013-12-23
David
van der Spoel
Fi
x
e
d co
m
pilation iss
u
e due to
g
cc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David van
d
e
r Spoel
More N
o
bel quotes
a
nd oth
e
rs
commit
|
commitdiff
|
tree
2013-11-07
Da
v
id van der Spoel
12 new
quotes
commit
|
commitdiff
|
tree
2013-09-30
David van der Sp
o
el
C
h
ange name of gmxdump to
d
ump and g
m
xc
h
e
c
k
to check
commit
|
commitdiff
|
tree
2013-09-29
David van der Spoel
Fixes b
u
g in processing
virtual_sitesn in gr
o
mpp
.
commit
|
commitdiff
|
tree
2013-09-26
Da
v
i
d
van d
e
r Sp
o
el
M
a
de MW of the Vsite particle
type
.
commit
|
commitdiff
|
tree
2013-09-21
Dav
i
d v
a
n der
Spo
e
l
M
o
ved n
g
mx to C++, renamed
i
t to view
.
commit
|
commitdiff
|
tree
2013-08-30
David van der Spoel
Updated g_clust
e
r
commit
|
commitdiff
|
tree
2013-07-24
David
v
a
n der Spoe
l
F
i
xes #1312 unin
i
tialized error in g_enemat
.
commit
|
commitdiff
|
tree
2013-07-17
David van
d
er S
p
oel
Added ci
t
ation to free volume paper
.
commit
|
commitdiff
|
tree
2013-06-14
Da
v
id van der Spoel
New an
a
lysis tool to compute the
fre
e
volume and
t
otal
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
David van
d
e
r Spo
e
l
Fixe
s
#1194 error reading 4
.
5
.
5 tpr fi
l
es wit
h
d
i
hres
commit
|
commitdiff
|
tree
2013-05-16
David
van der Spoel
Fi
x
ed two
co
m
pilat
i
on issues
.
commit
|
commitdiff
|
tree
2013-05-02
David van
der
Spoel
F
ixes #12
3
8 g_hydorder does no
t
call
s
et_pb
c
.
commit
|
commitdiff
|
tree
2013-05-01
Da
v
id van der Spoel
Merge
"Upda
t
ed source
f
or Van
d
er
W
a
a
ls rad
i
i
.
"
commit
|
commitdiff
|
tree
2013-04-25
Davi
d
van der S
p
oel
Upd
a
t
e
d
s
o
urce for
V
a
n der Waals r
a
dii
.
commit
|
commitdiff
|
tree
2013-03-07
D
a
vid v
a
n der
S
poel
Fixes #1183 PB
C
bug in g_mindist
commit
|
commitdiff
|
tree
2013-02-13
David van der Spoel
Pla
i
n
t
ext quotes
.
commit
|
commitdiff
|
tree
2013-01-11
David van der Spoel
Fixes #99
4
confu
s
i
o
n
in atomp
r
op
.
commit
|
commitdiff
|
tree
2012-11-26
David v
a
n d
e
r Spoel
Fixe
s
#1035 NaN in g_cluster output
.
commit
|
commitdiff
|
tree
2012-11-20
D
a
v
id va
n
d
e
r Spoel
Fixes bug in g_hbond that
makes it produce fa
t
al error
.
commit
|
commitdiff
|
tree
2012-11-12
David van der
S
poel
Fixe
s
#1020 o
p
tion
s
in g_enemat
commit
|
commitdiff
|
tree
2012-10-21
Da
v
id van
der
S
poe
l
Fixed Bug #593 about memory hole in trjcat
.
commit
|
commitdiff
|
tree
2012-10-04
David van der Spoel
S
e
t return val
u
e to FALSE (0) in estimate_dt in libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-15
David
v
an der
S
p
oel
Merge "Adap
t
ed NMR related data
t
o ne
w
pd
b
forma
t
.
.
.
.
commit
|
commitdiff
|
tree
2012-09-07
David van der Spoe
l
Adapted NMR
r
elated data to new pd
b
format
.
commit
|
commitdiff
|
tree
2012-09-04
David van der Spoel
Made
t
utorial
s
lightly less confusi
n
g
.
commit
|
commitdiff
|
tree
2012-08-16
David van der Spoel
Opti
o
na
l
comp
u
ta
t
ion of f
l
uct
.
props
i
n
g_energy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
D
avid va
n
der Spoel
F
i
xed bug
in free energy calcu
l
a
t
ion
f
or Morse potentials
commit
|
commitdiff
|
tree
2012-06-21
David van der Sp
o
e
l
F
i
xes
#
9
6
1 -
S
h
ake reports wrong error
commit
|
commitdiff
|
tree
2012-06-16
David van der Spoel
Fi
x
es #882 - looping bu
g
in trxio
.
c
commit
|
commitdiff
|
tree
2012-03-17
D
avid van d
e
r Spoel
R
e
moved qh
o
p
files from
t
his
bran
c
h
.
commit
|
commitdiff
|
tree
2012-03-10
David van der Spoel
Vibration spectra from velocity ACF or Nor
m
al modes
.
commit
|
commitdiff
|
tree
2012-01-31
D
a
vi
d
va
n
d
e
r Spoe
l
Changed order of parameters in top file
commit
|
commitdiff
|
tree
2012-01-25
David
v
an der Spo
e
l
Adde
d
two ne
w
bonded func
t
io
n
s
.
commit
|
commitdiff
|
tree
2012-01-17
David
van der Spoel
Replac
e
stde
r
r b
y
s
tdo
u
t in ed
i
tconf terminal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
D
a
vid van der Sp
o
el
Introd
u
ced fa
t
al
e
rr
o
r
i
n g
r
omp
p
for incorrect use
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
David van der Spoel
Com
m
ent
e
d
o
ut p
a
rt
o
f th
i
s new pr
o
gram that was n
o
t
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Dav
i
d van der S
p
oel
Fixed
d
ocumentatio
n
issue described
in re
d
m
ine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Da
v
i
d
van der Spoe
l
Fixed docu
m
entati
o
n is
s
ue described in redmin
e
i
s
s
u
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
David
v
a
n de
r
Spoel
Fixed co
m
pilation issues
commit
|
commitdiff
|
tree
2011-09-19
Da
v
id
van der Spoel
Resolved gerrit issu
e
https://gerrit
.
gromacs
.
org/
#
change,126
commit
|
commitdiff
|
tree
2011-05-23
D
avi
d
van der Spo
e
l
Re-i
m
pl
e
mented
the fluctuati
o
n analysis, b
a
se
d
o
n
En
t
halpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van
d
er Spoel
Re
-
implemented
t
he fluctuation
anal
y
sis,
based on Enthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
D
avid van der Sp
o
e
l
Merge branch 'release-
4
-5-
p
a
tches' of git
.
g
romacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
Davi
d
van
der Spoel
Added g_hydorder
.
1 man page
.
commit
|
commitdiff
|
tree
2011-04-06
David
van de
r
Spoel
F
ixed
header for gm
x
_conect_init
commit
|
commitdiff
|
tree
2011-04-06
David van der Spoel
Fi
x
ed he
a
der for gmx_con
e
ct_init
commit
|
commitdiff
|
tree
2011-04-04
David van
der Spoel
N
e
w entry
commit
|
commitdiff
|
tree
2011-01-22
Da
v
id van der Spoel
Fixe
d
bu
g
67
8
which was
d
u
e
to calling gmx_fa
t
a
l
w
i
th
o
ut
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van de
r
Spoel
Fi
x
ed bug 678 which was
due to calling gmx_fat
a
l withou
t
.
.
.
commit
|
commitdiff
|
tree
2010-12-23
David van d
e
r Spoel
M
erge bran
c
h
'
release-4-5-pa
t
ch
e
s'
commit
|
commitdiff
|
tree
2010-12-23
David van de
r
S
poel
Fi
x
ed b
u
g
i
n sta
t
istics which d
i
d
n
ot all
o
w fitting
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Dav
i
d van der Spoel
M
e
rge branc
h
'release-
4
-5-patches'
commit
|
commitdiff
|
tree
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