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MSD tests for the -mol option.
2019-01-14
Da
v
id van
d
e
r
Spo
e
l
M
S
D
t
e
sts
f
o
r the -mol option
.
commit
|
commitdiff
|
tree
2019-01-11
David van der Spoel
Added low-l
e
v
el t
e
st
s
for improper dihedrals
.
commit
|
commitdiff
|
tree
2018-12-31
David van der Spoel
Moved
generic simulationdatabase code to t
e
stutils
.
commit
|
commitdiff
|
tree
2018-12-30
D
av
i
d van der
Spoel
Moved
input fi
l
es f
o
r tests to simula
t
ion database
.
commit
|
commitdiff
|
tree
2018-12-30
Dav
i
d van der Spo
e
l
Implemente
d
native norma
l
mode analysis tests
.
commit
|
commitdiff
|
tree
2018-12-22
D
avid van der
S
p
oel
Revert
"
Remove
d
t_top
o
lo
g
y from
g
m
x msd"
commit
|
commitdiff
|
tree
2018-12-20
David van der Spoe
l
Rem
o
v
e
d
t_topology from gmx msd
commit
|
commitdiff
|
tree
2018-12-05
D
a
vid van der Spoel
Added
new t
e
sting code for norma
l
mode a
n
alysis
.
commit
|
commitdiff
|
tree
2018-12-04
David
v
an der Spoel
Sm
a
ll update to mdrun
tests
.
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
van
der Spoel
Removed
g
m
x
morph
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
v
a
n d
e
r
Spoel
Removed gmx
dyndom
commit
|
commitdiff
|
tree
2018-12-04
David v
a
n der Spo
e
l
Removed gmx anadoc
k
commit
|
commitdiff
|
tree
2018-11-21
David van der
S
p
oel
Merge branch 're
l
ease-2019'
commit
|
commitdiff
|
tree
2018-11-18
D
a
v
id
van der Spoel
Added cita
t
ion for
n
ew analysis func
t
ionali
t
y
.
commit
|
commitdiff
|
tree
2018-11-11
D
a
vid va
n
der Spoel
Fix en
t
ro
p
y calculation in gmx
anaei
g
commit
|
commitdiff
|
tree
2018-11-09
David van der
S
poel
Change get
_
atom
_
index t
o
allow multiple
m
olecules
.
commit
|
commitdiff
|
tree
2018-10-11
D
a
vid van der Spoel
R
e
instated quasiharmon
i
c
e
ntropy
calculation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
D
a
vid van der Spo
e
l
Added option to
g
m
x nmeig to print ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
Davi
d
van der Sp
o
el
Let g
m
x
n
m
e
ig prin
t
t
h
ermochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
D
a
v
i
d van der Spoel
Renamed entrop
y
.
*
to therm
o
chemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der Spoel
Split of
f
e
nt
r
opy
c
alcul
a
tion to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
David van der Spoe
l
Fix
e
s
and updates fo
r
xplor2gml
.
pl and at
o
m_no
m
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van der Spo
e
l
F
i
xed check fo
r
water
i
n gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David va
n
de
r
S
p
oel
New md
p
input
f
or e
l
ectric fiel
d
s
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoe
l
F
ix
e
d
mdp output fro
m
electric field code
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
an
d
er
S
poel
Added
option -water tips3
p
t
o pdb2gm
x
.
commit
|
commitdiff
|
tree
2017-10-23
David van d
e
r Spoel
Split
o
ff the NMR re
l
at
e
d
a
n
alyses fr
o
m
gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
avid van der
S
poel
Fixed missing entries in nrnb arra
y
s
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoe
l
Wor
k
e
d around m
i
ssing Op
e
nMP i
m
plementat
i
on i
n
ori
r
es
.
commit
|
commitdiff
|
tree
2017-08-03
D
avid v
a
n der
S
poe
l
Fixed bug in gmx
d
i
s
res
i
n
dexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
Dav
i
d van der Spoe
l
Worked ar
o
und
missing
O
p
enMP implementation in or
i
r
e
s
.
commit
|
commitdiff
|
tree
2017-07-28
Da
v
id van der Spoel
Added unit-tes
t
for or
i
ent
a
ti
o
n restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van
der S
p
o
e
l
R
e
moved unn
e
ce
s
sar
y
static dec
l
ar
a
tion
s
for comman
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van de
r
S
poel
Fixed
t
est-order depen
d
ency in g
m
xpreprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David v
a
n d
e
r Spoel
Fix
n
on-reproducab
i
lity of clust
s
i
ze
tests
.
commit
|
commitdiff
|
tree
2017-05-01
David
van
d
er Spoel
X
p
m te
s
t f
o
r gmx
c
lus
t
s
ize
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoel
Added tests for gmx clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David
v
an der
Spoel
Removes rogue print
i
ng to xvg fil
e
in gmx mindi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoe
l
Fixes bug i
n
gm
x
so
l
vate wi
t
h
-
shell that yielded
0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spo
e
l
Fix
e
s S
E
G
V
in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David van d
e
r Spoel
Only
print
a
ll dangling ato
m
s with
g
rompp -v
commit
|
commitdiff
|
tree
2017-01-23
David va
n
der Spo
e
l
Adde
d
r
e
ference for dihedr
a
l
function in O
P
L
S
.
commit
|
commitdiff
|
tree
2016-12-07
David va
n
der Sp
o
el
C
o
u
p
le of new quotes
commit
|
commitdiff
|
tree
2016-11-18
Da
v
id van
d
er S
p
oel
A
dded fi
r
st tes
t
s
o
f bonded
f
orce
fu
n
c
t
ions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der
S
poe
l
Fixes
s
ome mem
o
ry
l
eaks associated with t
e
s
ting a
p
plied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David va
n
der S
p
oel
Modularize electri
c
fiel
d
han
d
li
n
g
commit
|
commitdiff
|
tree
2016-09-27
David va
n
der Spo
e
l
Fixed
s
cri
p
t xplor2gm
x
.
pl to wo
r
k with
GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
D
a
v
i
d
va
n
der Spoel
F
ixe
s
issue with
R
ele
a
se bu
i
ld in c
o
r
re
l
at
i
on functio
n
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van
der Spoel
Made
c
o
r
rel
a
t
i
o
n
function routine use
s
t
d::vector
commit
|
commitdiff
|
tree
2016-08-24
D
avid
v
an d
e
r
Spoe
l
Added d
o
c
umentation
f
or shell potentials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der Spoel
T
hre
e
n
ew quot
e
s
.
commit
|
commitdiff
|
tree
2016-07-29
D
a
vid van
de
r
S
poe
l
Fixes
i
ncorrect charges
i
n
OPLS/AA-L for HISD and HIS
E
commit
|
commitdiff
|
tree
2016-07-08
D
avid van der Spo
e
l
Introduc
e
fatal error fo
r
too few frames in
g
mx
dos
.
commit
|
commitdiff
|
tree
2016-06-27
David
van der Spoel
Made
gmx
d
os wor
k
a
g
ain
.
commit
|
commitdiff
|
tree
2016-06-22
David van der
S
poe
l
Removed spurious
r_ij in forc
e
fo
r
Morse potentia
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der Spoel
Mod
i
fy lmfit library
t
o avoid c
l
ashe
s
w
i
t
h
other versions
.
commit
|
commitdiff
|
tree
2016-03-23
David
v
an d
e
r Spoel
Removed srenew that was ma
k
ing array smal
l
er incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
Da
v
id van
d
er S
p
oe
l
Fixe
d
division by zer
o
in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van
d
er Spoel
Co
u
ple of new q
u
otes
commit
|
commitdiff
|
tree
2016-01-07
David v
a
n de
r
Sp
o
el
Made n
o
r
m
a
l
modes
work with
s
hel
l
s and vsite
s
commit
|
commitdiff
|
tree
2015-11-24
David van der Sp
o
e
l
F
i
xes newly intr
o
du
c
ed bug
in
m
ake_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Spoe
l
Moved domd
e
c
s
t
ructure
s
out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van d
e
r Spoel
C
l
ea
n
ups in
le
g
ac
y
header/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
a
n
der Spoel
Merged lega
c
yheaders
/
types/q
m
mmrec
.
h in
t
o
mdli
b
/qm
m
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van
der Spo
e
l
Merged ge
n
b
o
rn
.
h from l
e
gacyhe
a
ders/t
y
pes into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Spoel
M
oved legac
y
hea
d
ers/types/grou
p
.
h
to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der Spoel
Merged legac
y
headers
/
typ
e
s/
n
s
.
h and nbl
i
st
.
h to
m
dty
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r
Sp
o
el
Combine enums
.
h
a
nd names*
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid
v
a
n
der Spo
e
l
Merged
legacyheaders/
n
rnb
.
h an
d
types/
n
rnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
e
r
S
p
oel
Moved
mdatom
.
h
from legacyhead
e
r/typ
e
s
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van
der Spoe
l
M
o
ved legacyhe
a
ders/typ
e
s/
e
n
e
rgy
.
h t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
va
n
der Spoel
Merged legacyheader
s
/types/inp
u
trec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Da
v
i
d va
n
der Spoel
Merged
legacyheader
s
/types/state
.
h into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d van de
r
Spoel
Replaced atom_i
d
by
int
.
commit
|
commitdiff
|
tree
2015-11-13
D
a
v
id van der Spoel
Mo
v
ed
g
enborn
.
h
to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van de
r
Spoel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
va
n
d
e
r Spoel
Move
d
copyrite
.
* to fileio from gmxli
b
an
d
legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der S
p
o
e
l
Moved in
p
utrec
.
* from gmxlib
a
nd legacyhead
e
rs to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
David
va
n
der Spoe
l
Removed
lega
c
yheaders/ty
p
ed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Davi
d
van
d
er Spoel
Moved
df
_
histo
r
y utility r
o
utines fro
m
typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Davi
d
van der
S
p
oel
R
ep
l
a
c
ed NOTSET
fro
m
typedef
s
.
h by local
solutions
.
commit
|
commitdiff
|
tree
2015-10-23
D
a
v
id van der Spoel
Removed e
n
ergyhistory co
d
e from
t
yped
e
fs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Moved pbc/cut-off related utilities
from
typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Fre
e
d memory in legacy sta
t
ist
i
cs
r
out
i
nes
.
commit
|
commitdiff
|
tree
2015-10-03
David van
d
er Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van d
e
r Sp
o
el
Removed simple
.
h f
r
om nb_ke
r
nel_sse4_1_X
X
commit
|
commitdiff
|
tree
2015-10-02
David va
n
der Sp
o
el
Removed s
i
mple
.
h from nb_k
e
r
n
el
_
sse2_
X
X
commit
|
commitdiff
|
tree
2015-10-02
D
avid
v
a
n
der Sp
o
el
Removed
s
imple
.
h from nb_kernel_c and
n
b
_k
e
rnel_spar
c
64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remove
d
inc
l
ude
s
imple
.
h from nb
_
k
erne
l
_
avx
_
128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
der Spoel
Removed simple
.
h
from nb_kerne
l
_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
i
d
v
an
der Spoel
Removed output_env_t, n
o
w us
i
ng gmx_output_e
n
v
_
t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spoe
l
Remo
v
ed types/
n
rnb
.
h from
t
ypede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d
v
an der S
p
oel
Removed types/nbli
s
t
.
h
and
ty
p
es/
n
sgrid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van der Sp
o
el
Removed types/
m
dat
o
m
.
h f
r
om typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van d
e
r Spoel
Remove
d
types
/
inputr
e
c
.
h from typedefs
.
h a
n
d
r
e
leted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van d
e
r
S
p
o
e
l
Fi
x
es
bug in the com
p
u
t
a
tion of Coef
f
ic
i
en
t
of Th
e
r
m
al
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
avi
d
va
n
der Spoel
Remo
v
ed types/forcerec
.
h from ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Rem
o
v
e
d
includ
e
o
f
t
y
pe
s
/
i
f
unc
.
h from typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Sp
o
el
Rem
o
ved four includ
e
s from
legacyheaders/typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
Remo
v
ed legacyhe
a
ders/type
s
/commrec_
f
wd
.
h
from t
y
pedef
.
h
commit
|
commitdiff
|
tree
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