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Cosmetic fixes to mdp documentation
2018-03-21
David van der Spoel
R
e
n
a
me
d
e
n
tropy
.
* t
o
the
r
mochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der Spoe
l
Split off entropy
c
a
lcu
l
at
i
on
t
o separate
f
ile
.
commit
|
commitdiff
|
tree
2017-12-28
Dav
i
d van
d
er
Spoel
F
i
xes and upd
a
t
es for
x
p
lor2g
m
l
.
pl and at
o
m_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van der S
p
oel
Fixed check f
o
r wa
t
er i
n
g
en
_
vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
D
a
v
i
d va
n
d
e
r
Spoe
l
New m
d
p inp
u
t for electr
i
c fields
.
commit
|
commitdiff
|
tree
2017-10-30
David
va
n
der
S
poel
Fixed
m
d
p o
u
tpu
t
f
rom el
e
ctric f
i
el
d
c
ode
.
commit
|
commitdiff
|
tree
2017-10-30
Davi
d
van d
e
r
S
poel
A
dded
option
-water tips3p
t
o pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van de
r
Spoel
S
plit
o
ff t
h
e NMR re
l
ated an
a
l
y
ses from g
m
x en
e
rgy
.
commit
|
commitdiff
|
tree
2017-10-17
David van d
e
r
S
poel
Fixed missi
n
g entries in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-08-15
D
a
v
id van der Spoel
Worked around missing OpenMP imp
l
ementati
o
n in orires
.
commit
|
commitdiff
|
tree
2017-08-03
D
avid van der S
p
oel
Fixed bug in
g
mx disre
s
inde
x
i
n
g arra
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
Da
v
i
d
va
n
der Spoe
l
Wor
k
ed aroun
d
missing OpenMP implementa
t
ion
in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David van der Spoel
Added uni
t
-test fo
r
orientation restraints o
u
tpu
t
.
commit
|
commitdiff
|
tree
2017-07-19
David va
n
der S
p
oel
Remo
v
ed u
n
n
e
cessa
r
y static decl
a
r
atio
n
s f
o
r command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David va
n
der
S
poel
Fixed tes
t
-order
d
e
pendency in gm
x
pr
e
process
t
ests
.
commit
|
commitdiff
|
tree
2017-07-19
David van d
e
r Spoel
Fi
x
non-re
p
ro
d
u
c
ability of
clustsize test
s
.
commit
|
commitdiff
|
tree
2017-05-01
David va
n
der
S
p
o
e
l
Xpm test for gmx clustsiz
e
commit
|
commitdiff
|
tree
2017-03-12
David van
der S
p
oel
Add
e
d t
e
s
t
s
for
g
mx clu
s
ts
i
ze
.
commit
|
commitdiff
|
tree
2017-03-04
Da
v
i
d
van der Spoel
Re
m
oves
ro
g
ue prin
t
i
n
g
to xvg fi
l
e in gmx
m
indi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David van
der Spoe
l
Fixes bug in gmx
s
ol
v
ate
with
-sh
e
l
l
that yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spoel
Fixes
SEGV in gmx or
d
er
.
commit
|
commitdiff
|
tree
2017-02-02
David van der Spoe
l
Only print all
dangling a
t
oms with grom
p
p -v
commit
|
commitdiff
|
tree
2017-01-23
Da
v
id van der Spoel
Ad
d
ed
re
f
er
e
nce f
o
r d
i
h
e
dral fun
c
tion in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
Da
v
id van
d
er S
p
oe
l
Coupl
e
o
f
n
ew quotes
commit
|
commitdiff
|
tree
2016-11-18
D
a
vi
d
van der
S
p
o
el
Added first tests of bonded forc
e
functio
n
s
.
commit
|
commitdiff
|
tree
2016-10-14
David van der Sp
o
el
Fixes some mem
o
ry lea
k
s asso
c
ia
t
ed wi
t
h testing appli
e
d
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der
Sp
o
e
l
Modulari
z
e elec
t
ric field handling
commit
|
commitdiff
|
tree
2016-09-27
David van
d
e
r Spoe
l
Fix
e
d script xplo
r
2gm
x
.
pl to work wi
t
h GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
D
a
vid van der Spoel
Fi
x
es issue with Rele
a
s
e build in correl
a
tion functions
.
commit
|
commitdiff
|
tree
2016-09-20
Dav
i
d van der Spoel
Ma
d
e
correlation function
r
out
i
ne
u
se st
d
::vector
commit
|
commitdiff
|
tree
2016-09-05
David van
der Sp
o
el
Merge "Mer
g
e branch release
-
2
016"
commit
|
commitdiff
|
tree
2016-08-24
Dav
i
d van der
S
p
oel
A
dded documen
t
ation for sh
e
ll po
t
entials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der
Spoel
Three new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David va
n
der Spo
e
l
Merge "Merge b
r
anch
release-5-1
i
n
t
o
release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van der Spoel
Fixes incorrec
t
c
h
arg
e
s in OPLS/AA
-
L for HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
Merge "Me
r
ge branch release-5-1
into
r
ele
a
se-20
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David v
a
n der
S
poe
l
I
n
t
roduce
fata
l
error f
o
r too few f
r
ames
i
n gmx
d
o
s
.
commit
|
commitdiff
|
tree
2016-06-27
David
v
an der Spoel
Made gmx dos work aga
i
n
.
commit
|
commitdiff
|
tree
2016-06-22
David va
n
der S
p
oel
Removed spu
r
ious
r
_ij in fo
r
ce
for Morse
potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
a
vid van der S
p
oel
Modify
l
mfit libra
r
y to a
v
oi
d
clas
h
es with other v
e
r
s
ions
.
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d van der
S
p
o
el
Removed srenew
t
ha
t
was making arra
y
sm
a
ller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David va
n
der S
p
o
el
Fixed d
i
v
ision by zero in polari
z
e
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Spoel
C
o
uple of new quote
s
commit
|
commitdiff
|
tree
2016-01-07
Davi
d
van der Spoel
M
ade normal mod
e
s work w
i
th shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
D
avid
van der Sp
o
el
Fixes newly int
r
oduced bug in
m
ake_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David v
a
n der Spoel
Move
d
d
omdec structure
s
out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoel
Cleanups in leg
a
cyhea
d
er/typ
e
s
/
commr
e
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
David v
a
n
d
er Spoel
Merged legacyheaders/types/qmmmrec
.
h into
m
d
lib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van d
e
r Spoel
M
erged genborn
.
h
from
legacyhe
a
der
s
/types int
o
mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der
Spoel
Moved l
e
gacyh
e
a
ders/types/group
.
h to
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
poe
l
Merged legacyheade
r
s/ty
p
es/n
s
.
h and nblist
.
h t
o
m
d
types
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Sp
o
el
C
ombine
enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged legacyheaders/nrnb
.
h and
t
ypes/nrnb
.
h to gmxl
i
b
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n der
S
poel
M
o
ved mdatom
.
h fro
m
lega
c
yheader/types
t
o
m
d
t
ype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Sp
o
e
l
Moved legacyheaders/types/en
e
rgy
.
h
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoe
l
Me
r
ged legacyh
e
a
d
ers/types/inp
u
tr
e
c
.
h
i
nto mdtyp
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van
d
er Spoel
Merged
legacyhea
d
ers/types/state
.
h into
mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Replaced atom_i
d
by int
.
commit
|
commitdiff
|
tree
2015-11-13
D
av
i
d van der Sp
o
el
M
oved genbor
n
.
h to
mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
avid v
a
n
der S
p
o
el
Move
d
txtdump
.
* to
f
ilei
o
.
commit
|
commitdiff
|
tree
2015-11-12
Da
v
i
d
v
a
n de
r
Spo
e
l
Moved copyrite
.
* to
fileio from gmxli
b
and leg
a
cyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
Dav
i
d
v
a
n
der
S
poel
Moved inputrec
.
* from gmx
l
ib and legacyheade
r
s to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Removed le
g
acyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David
v
a
n der S
p
oel
M
oved df_his
t
or
y
ut
i
lity r
o
utines from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spo
e
l
Replaced NOTSET from typedefs
.
h by l
o
ca
l
s
olut
i
ons
.
commit
|
commitdiff
|
tree
2015-10-23
David van der
S
poe
l
Remov
e
d energyhistory cod
e
from type
d
efs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
D
a
vid van der
Spoel
Moved pb
c
/cut-
o
ff related utiliti
e
s
f
rom t
y
pedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der
S
poel
Fre
e
d me
m
o
ry in l
e
gacy statis
t
ics
r
ou
t
in
e
s
.
commit
|
commitdiff
|
tree
2015-10-03
David
v
an der Sp
o
el
Removed simp
l
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David va
n
der Spoel
Removed
simp
l
e
.
h
f
r
o
m nb_kernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David
v
an der Spoel
R
emoved simple
.
h from nb_k
e
r
nel_ss
e
2_XX
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n
d
e
r Spoel
Removed simple
.
h from
nb
_
kern
e
l_c and nb_kernel_sparc
6
4_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
p
o
e
l
Removed
include simpl
e
.
h from n
b
_kernel_av
x
_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
de
r
Spo
e
l
Removed sim
p
le
.
h
from n
b
_
kernel_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
der Sp
o
e
l
Removed output_env_t, no
w
using gm
x
_output_en
v
_
t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van
d
er Spoel
Remove
d
t
ypes/n
r
nb
.
h
fr
o
m
typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der
Spoel
Removed types/nb
l
ist
.
h and types/nsgrid
.
h
f
rom typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van der Spoel
Removed
types
/
mdatom
.
h f
r
om t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
van der Spoel
R
emo
v
ed type
s
/inputrec
.
h from typ
e
d
e
fs
.
h
a
nd releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David va
n
der Spoel
Fix
e
s bug in the computation of Coef
f
i
c
i
ent of T
h
er
m
al
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
Davi
d
van
der Spoel
Removed ty
p
es/forcerec
.
h from
t
ype
d
ef
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
D
a
vid van
der Spoel
Removed i
n
clude of ty
p
e
s
/ifunc
.
h from
t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David va
n
der Spoel
Removed four in
c
ludes from legacyheaders/t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Dav
i
d
van der Spoel
Removed legacyh
e
a
d
ers
/
t
y
pes/commrec_fwd
.
h
f
rom typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
an der
Spoel
Moved content from
mdrun
.
h to sep
a
rate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoe
l
Re
m
ov
e
d <sys/
t
ypes
.
h> and "types/cons
t
r
.
h" fr
o
m typedefs
commit
|
commitdiff
|
tree
2015-09-09
D
a
v
i
d van
d
e
r Spoel
Removed fileio/trx
.
h fro
m
typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
van der Spoel
M
oved function
s
operating on
f
orcerec to separate hea
d
er
.
commit
|
commitdiff
|
tree
2015-08-28
Davi
d
v
an der Spoe
l
Added
energy
(
e
d
r) file t
y
pe to
Options head
e
rs
.
commit
|
commitdiff
|
tree
2015-08-28
Da
v
id van d
e
r Spoel
Added add
i
t
ional cons
t
ructor
to StringSt
r
eam class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van der Spoel
Made output from dumping nei
g
htborlists
e
asier to read
.
commit
|
commitdiff
|
tree
2015-07-31
Da
v
id van der
S
poel
Change i
n
i
ti
a
l paramete
r
s for t
e
sting expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David v
a
n
d
e
r Spoel
Code
for checking xvg files
in
testutils
.
commit
|
commitdiff
|
tree
2015-04-17
David van der
S
poel
Updated exponential fitting to make it r
o
bus
t
.
commit
|
commitdiff
|
tree
2015-04-09
Da
v
id
v
an der Sp
o
e
l
Clarified comme
n
ts for time-dependent ele
c
tric fields
.
commit
|
commitdiff
|
tree
2015-04-08
David v
a
n der
Spo
e
l
Fixe
d
incorrect output of gb_algorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David
v
an der
Spoel
Updated documentat
i
on for elec
t
ric fields
.
commit
|
commitdiff
|
tree
2014-12-13
Da
v
id
v
a
n
de
r
Spoel
Four
new quotes
from ar
o
und the wo
r
ld
.
commit
|
commitdiff
|
tree
2014-11-28
D
a
vid van der Spoel
F
ixes r
e
ce
n
tly
introdu
c
e
d bug
i
n gmx anal
y
ze
.
commit
|
commitdiff
|
tree
2014-11-24
David van der Spoel
Added wa
r
nings
f
or
ewald-
g
eometry
a
nd s
u
rfac
e
-epsil
o
n
commit
|
commitdiff
|
tree
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