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MSD tests for the -mol option.
2015-09-25
David van der Spoel
R
e
m
oved include of types
/
ifunc
.
h from typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der
Sp
o
e
l
Removed f
o
ur includes fr
o
m
l
egacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van
d
er Spoel
Removed l
e
gacyheaders/types/com
m
rec_fwd
.
h
from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
D
a
vid van de
r
Spoe
l
M
oved c
o
ntent from
mdrun
.
h to sep
a
rate
headers
.
commit
|
commitdiff
|
tree
2015-09-10
Davi
d
van der Spoel
Re
m
oved
<sys/ty
p
es
.
h> and "types/
c
ons
t
r
.
h" f
r
om typedefs
commit
|
commitdiff
|
tree
2015-09-09
David van d
e
r
Spoel
Removed fileio/trx
.
h
f
r
om typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van de
r
Spoel
M
o
ved f
u
n
ctions opera
t
ing on
forc
e
r
e
c to
separate header
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
Added energy (edr) f
i
le type to Options header
s
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
A
dded additi
o
nal
c
onstru
c
t
o
r t
o
StringStream c
l
ass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
Dav
i
d van der
Spoel
Ma
d
e output
f
rom
d
umping neightborl
i
sts easi
e
r to rea
d
.
commit
|
commitdiff
|
tree
2015-07-31
David van
der Spoel
Change initial pa
r
amet
e
rs
fo
r
testing
e
xpfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoel
C
ode
for checking xvg files
in t
e
stutils
.
commit
|
commitdiff
|
tree
2015-04-17
D
avid van der
S
po
e
l
Update
d
ex
p
onenti
a
l
fitting to
m
ake it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David v
a
n
d
e
r Spoel
Clarified co
m
men
t
s for
t
ime
-
depende
n
t electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
Da
v
id
v
a
n
d
er Spoel
Fixe
d
incorrect output
of gb_a
l
gorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
D
a
vid
van der Spoel
Updated docu
m
entation f
o
r
electric fie
l
ds
.
commit
|
commitdiff
|
tree
2014-12-13
David van d
e
r Spoel
Four
n
ew quotes from
a
round the
w
o
rld
.
commit
|
commitdiff
|
tree
2014-11-28
David van der
S
po
e
l
Fixes recently
introduced bug in g
m
x analyze
.
commit
|
commitdiff
|
tree
2014-11-24
D
a
vid van
de
r
Spoel
Added
w
arnings for ewald-geometry
a
n
d su
r
face-epsilon
commit
|
commitdiff
|
tree
2014-10-28
David van
d
e
r
Spoel
Even more refresh
i
ng quot
e
s
.
commit
|
commitdiff
|
tree
2014-10-14
D
avid van de
r
Spoel
Reorganizing analysis
o
f correlation functions
.
commit
|
commitdiff
|
tree
2014-09-23
David v
a
n de
r
Sp
o
el
F
i
xes potential b
u
g in neighbor
s
earching
.
commit
|
commitdiff
|
tree
2014-09-17
David v
a
n
der Sp
o
el
Merge re
l
e
ase
-
5-0 into master
commit
|
commitdiff
|
tree
2014-09-10
D
avid
v
an der Spoel
Remove
.
tpa,
.
tpb
,
.
tpx,
.
trj file
s
.
Part of
#
1500
.
commit
|
commitdiff
|
tree
2014-08-30
David van der Spoel
Fixes issue with vsiten and verlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van der S
p
o
el
Fixe
d
i
ncons
i
s
t
e
n
cy in blocka handli
n
g
.
commit
|
commitdiff
|
tree
2014-06-29
David van d
e
r Spoel
Fixes #
1
532, SEGV in g
_
curr
e
n
t
.
commit
|
commitdiff
|
tree
2014-06-25
David van der Spoel
A
d
ded check for domain de
c
omposition
a
nd
shells
.
commit
|
commitdiff
|
tree
2014-06-24
D
avi
d
v
an der Spoe
l
A
d
d
e
d check in gro
m
pp for
s
he
l
ls and i
n
putrec
i
ssues
.
commit
|
commitdiff
|
tree
2014-06-22
Dav
i
d
van
d
er Spoel
Implement
e
d fatal error
f
or nst
c
al
c
energ
y
!=1 with she
l
ls
.
commit
|
commitdiff
|
tree
2014-06-13
Davi
d
van der Spoel
Fix mem
o
ry-usage
error in g_chi
commit
|
commitdiff
|
tree
2014-06-11
David van
d
e
r
Spoel
Fixes
b
ug where -e and
-dt fla
g
s di
d
not
work anym
o
re
.
commit
|
commitdiff
|
tree
2014-06-07
David van der Spoel
Me
r
ge "
M
erge
r
e
lease-5-0 i
n
to ma
s
ter"
commit
|
commitdiff
|
tree
2014-06-07
D
a
v
id van der Spoel
Merge releas
e
-5
-
0 into mas
t
er
commit
|
commitdiff
|
tree
2014-06-02
David v
a
n der Sp
o
el
Fixed
wr
o
n
g
journa
l
reference in manua
l
commit
|
commitdiff
|
tree
2014-05-31
David van der Spoel
Per
m
i
t
trjconv to read an
d
write
ve
l
ocities w
i
t
h TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van
d
er Spoel
Fixes a co
m
plicated bug
i
n g_anaeig
.
commit
|
commitdiff
|
tree
2014-05-15
David v
a
n
der Spo
e
l
Added cmake prof
i
ling su
p
port
commit
|
commitdiff
|
tree
2014-04-02
David
van der Spoel
Remove
d
pos
s
ibil
i
ty of
compiling
w
ith GSL
.
commit
|
commitdiff
|
tree
2014-03-31
D
a
vid van der S
p
oel
Fixed c
o
mpilation
i
ssue in fgrid
.
cpp due
to int/enum
commit
|
commitdiff
|
tree
2014-03-06
David van
d
er Spoel
Six
n
ew quotes from classic literature
.
commit
|
commitdiff
|
tree
2014-02-11
David van der Spoel
Fi
x
e
d
another vmd
i
o issue
.
commit
|
commitdiff
|
tree
2014-02-10
David van der Spo
e
l
M
oved conditional cmake code for vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
Davi
d
v
a
n der Spoel
Mo
v
ed
ran
d
om number gen
e
rator code to separate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David van der
S
poe
l
This patch moves
t
he statistics library to
its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David van der Spoel
This patch mo
v
es preprocessing h
e
aders to gmxp
r
e
p
rocess
commit
|
commitdiff
|
tree
2014-01-15
David van
der Spoel
This p
a
t
c
h move
s
the nrama
.
[c
h
] to
t
he g
m
xana dir
.
commit
|
commitdiff
|
tree
2014-01-13
David van der
Spoel
Cleane
d
u
p
list of GROMACS authors
commit
|
commitdiff
|
tree
2014-01-09
David va
n
der Spoel
Fi
x
ed precision in the
r
mal
e
xpansion coeffici
e
nt calc
.
commit
|
commitdiff
|
tree
2013-12-23
David van de
r
S
poel
Fixe
d
compilation i
s
sue due to gc
c
4
.
8
commit
|
commitdiff
|
tree
2013-12-21
D
avid
v
an
de
r
S
poel
More Nobel quot
e
s
a
n
d oth
e
rs
commit
|
commitdiff
|
tree
2013-11-07
David van der Spoel
12 new quo
t
es
commit
|
commitdiff
|
tree
2013-09-30
Dav
i
d van der Spoel
Change name
of gmxdu
m
p
t
o d
u
mp and
g
m
xcheck to check
commit
|
commitdiff
|
tree
2013-09-29
David van de
r
Spoel
Fixes bu
g
in pr
o
c
e
ss
i
ng
v
irtual_sitesn in grompp
.
commit
|
commitdiff
|
tree
2013-09-26
David van der S
p
oel
Made MW of the
Vsite partic
l
e type
.
commit
|
commitdiff
|
tree
2013-09-21
Da
v
id van der Sp
o
el
M
oved ngmx to C++, renamed it to vi
e
w
.
commit
|
commitdiff
|
tree
2013-08-30
David van der Sp
o
e
l
Updated
g
_clu
s
ter
commit
|
commitdiff
|
tree
2013-07-24
D
avid van der Spoel
Fixe
s
#1312 unin
i
tial
i
ze
d
e
rror in g_en
e
mat
.
commit
|
commitdiff
|
tree
2013-07-17
Dav
i
d van der
S
poel
Add
e
d
cit
a
t
i
on to
f
ree
v
ol
u
me paper
.
commit
|
commitdiff
|
tree
2013-06-14
David van d
e
r
Spoel
New analys
i
s tool to compute the free
volume and to
t
al
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
D
avid van de
r
Sp
o
el
Fixes #1194 err
o
r
reading
4
.
5
.
5 tpr f
i
l
e
s with
dihres
commit
|
commitdiff
|
tree
2013-05-16
Davi
d
van der Spoel
F
ixed two com
p
ilation issues
.
commit
|
commitdiff
|
tree
2013-05-02
Da
v
id van der Spoel
Fixes #12
3
8 g_hy
d
order doe
s
not call set_pbc
.
commit
|
commitdiff
|
tree
2013-05-01
David van der Spoel
Mer
g
e "Up
d
a
ted s
o
urce for Van der Waals ra
d
ii
.
"
commit
|
commitdiff
|
tree
2013-04-25
David van der
S
poel
Updated source for Va
n
der Waals radii
.
commit
|
commitdiff
|
tree
2013-04-16
David v
a
n
d
er Spoel
Me
r
g
e
"corrected
gro
m
pp
r
vdw
c
harge
-
g
r
oup radii chec
k
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David van der
S
poel
M
e
r
g
e
"a
d
ded mdrun check f
o
r Verlet+perturb
e
d atoms
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
David van d
e
r Spoel
Merge "Add histogram out
p
ut
for 'gmx ga
n
gle'
.
"
commit
|
commitdiff
|
tree
2013-03-07
David van der Spoel
Fixes #1183 PBC bug in g_mind
i
st
commit
|
commitdiff
|
tree
2013-02-15
Dav
i
d
v
an
der Sp
o
el
Merge "Fix
e
d a
n
initializ
a
tion issue in gmx_d
i
poles
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
David van der Spoel
Pl
a
in text quo
t
es
.
commit
|
commitdiff
|
tree
2013-01-14
David
van
der
S
p
oel
Merge "Fixi
n
g trj
c
o
n
v
-sub
"
into
release-4-5-p
a
t
c
hes
commit
|
commitdiff
|
tree
2013-01-14
David van der Spoel
Merge "Noting th
a
t and why gmxdum
p
-
s
-sys is
broke
n
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
D
a
v
i
d van
d
e
r Sp
o
el
F
i
xes #994
confusion in a
t
omprop
.
commit
|
commitdiff
|
tree
2013-01-07
D
a
vid van der
S
poel
Merge "Remove
d
reference to nonexistent
file i
n
g_helix
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
Davi
d
van
der Spoel
Merge "Merge
release-4-5-patches into releas
e
-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
David van
d
er Spo
e
l
Fixe
s
#1035 NaN in g_cluste
r
output
.
commit
|
commitdiff
|
tree
2012-11-20
David
v
an der Spoel
Fix
e
s bug
in g_h
b
ond that makes
it p
r
odu
c
e
f
atal erro
r
.
commit
|
commitdiff
|
tree
2012-11-17
Da
v
id
van der Sp
o
el
Merge "Add
e
d grompp w
a
r
ning
"
into relea
s
e-4-6
commit
|
commitdiff
|
tree
2012-11-17
D
a
vid van de
r
Sp
o
el
Me
r
ge "Remov
e
res
t
of the xml support" i
n
to release-
4
-6
commit
|
commitdiff
|
tree
2012-11-16
D
a
vid
v
an de
r
Sp
o
el
Merge "Remo
v
es unused fil
e
s
"
i
n
to rel
e
ase-4-6
commit
|
commitdiff
|
tree
2012-11-12
Davi
d
van der
Spo
e
l
F
ixes #1020 options in
g
_e
n
emat
commit
|
commitdiff
|
tree
2012-10-26
David van der Spoel
Merge
"
Fixed Pulp Fiction
quote" in
t
o
r
elease-4-5-patche
s
commit
|
commitdiff
|
tree
2012-10-21
David van der
Spo
e
l
Fixed Bu
g
#593
a
bo
u
t memory hole
in trjcat
.
commit
|
commitdiff
|
tree
2012-10-13
David van de
r
Spoel
Merge "Fixing
i
s
s
ues with replica exchange" into
r
elease-
4
-6
commit
|
commitdiff
|
tree
2012-10-12
David van der Spoel
Merge "[
t
ools] g_sans
- add traj
e
ctory avereg
i
ng"
commit
|
commitdiff
|
tree
2012-10-04
David van der Spoel
Set re
t
u
r
n value to F
A
LSE (0)
in estima
t
e_dt
i
n libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-15
David van d
e
r
Spo
e
l
Merge
"
Adap
t
ed NMR rel
a
te
d
da
t
a to
n
ew
p
db f
o
rma
t
.
.
.
.
commit
|
commitdiff
|
tree
2012-09-07
David van
d
e
r Spoel
Ada
p
ted NM
R
related
d
ata to new pdb format
.
commit
|
commitdiff
|
tree
2012-09-04
David va
n
d
e
r
Sp
o
el
M
ade
t
utoria
l
slightly less conf
u
s
i
ng
.
commit
|
commitdiff
|
tree
2012-08-16
Davi
d
v
an der Spoel
Opt
i
o
nal computa
t
i
on of fluct
.
props i
n
g
_
e
n
ergy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-07-15
David van der Spoel
M
erge "Autogenera
t
e gr
o
macs
.
7 fro
m
programs
.
t
x
t" into
.
.
.
commit
|
commitdiff
|
tree
2012-07-05
David van de
r
Spo
e
l
Merge "Improve Pro
g
ra
m
Info and u
s
e i
t
e
v
erywhere
.
"
commit
|
commitdiff
|
tree
2012-06-30
David va
n
der Sp
o
el
Fi
x
ed bug in free energy calc
u
lation
fo
r
M
o
r
s
e pote
n
t
i
a
l
s
commit
|
commitdiff
|
tree
2012-06-21
Da
v
id van der Spoel
Fixes #96
1
- Shake r
e
port
s
wrong er
r
or
commit
|
commitdiff
|
tree
2012-06-16
Dav
i
d van der Spoel
Fi
x
es #8
8
2 - looping bu
g
in trxio
.
c
commit
|
commitdiff
|
tree
2012-05-27
David van der Spoel
Merge "added expli
c
it
s
qrtf to the float ve
r
s
ion
of
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
Dav
i
d v
a
n de
r
Spoel
Merg
e
"grompp
n
ow re
t
a
i
ns the or
d
er o
f
bonds converted
.
.
.
commit
|
commitdiff
|
tree
2012-05-03
David
van de
r
S
po
e
l
Merge
"
Remo
v
e
d
unused code from s
r
c
/ke
r
nel/
.
"
commit
|
commitdiff
|
tree
2012-04-29
David van d
e
r
S
poel
Merge "chang
e
d number of iatoms for F_SET
T
LE from
1
.
.
.
commit
|
commitdiff
|
tree
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