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Cosmetic fixes to mdp documentation
2018-03-21
D
a
vid
v
an der Spoel
Renamed entrop
y
.
* to the
r
mochemist
r
y
.
*
commit
|
commitdiff
|
tree
2018-03-16
Da
v
id van der Sp
o
el
Sp
l
it off entropy calculation
t
o sep
a
ra
t
e
fi
l
e
.
commit
|
commitdiff
|
tree
2017-12-28
D
a
vid van der
S
poel
Fixes and
u
pd
a
tes for xplor2gml
.
pl and atom
_
nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van
der Spoel
Fixed check
f
or water in gen_
v
site
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van der
S
poel
New mdp input for e
l
ect
r
ic fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van
der S
p
o
el
Fixed mdp output
f
rom electric field cod
e
.
commit
|
commitdiff
|
tree
2017-10-30
David va
n
der Spoel
Added option -water ti
p
s3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van der Spoel
Split
o
ff the
NMR related analyses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van d
e
r Spoel
Fixed miss
i
ng
e
ntries in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoel
Worked
around m
i
ssi
n
g OpenMP
i
mplementatio
n
in orire
s
.
commit
|
commitdiff
|
tree
2017-08-03
Da
v
id van der Spoe
l
Fixed
b
u
g
in gm
x
disr
e
s
indexing
a
rrays
.
commit
|
commitdiff
|
tree
2017-08-02
D
a
v
i
d van der Spoel
Worked
a
ro
u
nd
m
issing O
p
enMP implem
e
nt
a
tion in ori
r
es
.
commit
|
commitdiff
|
tree
2017-07-28
David van
der Spoel
Added unit-test for ori
e
ntation restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
David v
a
n
der Spoe
l
Removed unn
e
cessary static
declaratio
n
s f
o
r command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
an der Spoel
Fixed te
s
t-order dependenc
y
in
g
m
x
p
re
p
rocess test
s
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid
van
der Spoel
Fix non-repro
d
ucability of
clustsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
David
v
an der Spoe
l
X
p
m test for gmx
clust
s
i
ze
commit
|
commitdiff
|
tree
2017-03-12
Davi
d
v
an
der Spoel
Adde
d
tests for gm
x
clu
s
tsize
.
commit
|
commitdiff
|
tree
2017-03-04
David
v
an d
e
r
S
poel
Rem
o
ves rogue
p
rinting to xvg file
in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
Davi
d
van der Spoel
Fixes bug in
gmx solvate with -shell that yielded
0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David
van der S
p
o
el
Fixes SEGV in g
m
x ord
e
r
.
commit
|
commitdiff
|
tree
2017-02-02
Davi
d
van
d
e
r Spo
e
l
Only pri
n
t
a
l
l
d
a
ngling atoms wi
t
h
grompp -v
commit
|
commitdiff
|
tree
2017-01-23
David van d
e
r
Spoel
Added reference
for
d
ihedra
l
function in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David
v
an der
S
poe
l
C
ouple
o
f
new quotes
commit
|
commitdiff
|
tree
2016-11-18
D
avid van der Spo
e
l
A
d
ded first t
e
sts of
b
o
n
ded force functi
o
ns
.
commit
|
commitdiff
|
tree
2016-10-14
David van
d
er Spoel
Fixes some memory lea
k
s ass
o
c
i
ate
d
wi
t
h tes
t
ing applie
d
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
Davi
d
van der Spo
e
l
M
odular
i
ze electric fiel
d
handling
commit
|
commitdiff
|
tree
2016-09-27
Dav
i
d
v
an der Spoel
F
i
xed scr
i
pt xplor2gmx
.
pl to wo
r
k w
i
th G
M
X
DATA
commit
|
commitdiff
|
tree
2016-09-26
David van der Spoel
F
ixes
is
s
ue with Release build in corr
e
l
a
tion function
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van der
Spoel
Made correlation function routine use std::
v
ector
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Merge "Merge branc
h
release-2016"
commit
|
commitdiff
|
tree
2016-08-24
Dav
i
d
v
an der Spoel
Add
e
d documenta
t
ion for shell
p
otentials
.
commit
|
commitdiff
|
tree
2016-08-03
Davi
d
va
n
der
Spoel
Three n
e
w
q
uotes
.
commit
|
commitdiff
|
tree
2016-07-31
David
van
d
e
r Spoe
l
Merge
"Merge branch relea
s
e-
5
-
1
into releas
e
-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
a
vid
van d
e
r Spoel
Fixes incorrec
t
charges
in OPLS/AA
-
L for HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
M
e
rge "M
e
rge branch relea
s
e
-
5-1 into rele
a
se-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Davi
d
van der Sp
o
el
Introduce f
a
tal e
r
ror for too few fram
e
s
i
n gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
Davi
d
van
d
er Spoel
Made
gmx
d
os
w
ork a
g
ai
n
.
commit
|
commitdiff
|
tree
2016-06-22
David van
d
e
r Spoel
Removed spur
i
ous r_ij in fo
r
ce fo
r
Mors
e
potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David
v
an der Spoel
M
od
i
fy
l
mfit library t
o
avoid cl
a
shes with other versi
o
ns
.
commit
|
commitdiff
|
tree
2016-03-23
David van
der Spoel
Removed srenew t
h
at
w
as
m
a
k
ing arr
a
y smaller
inc
o
rre
c
tly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Spoel
Fixed div
i
sion
b
y zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Sp
o
el
Couple of new
q
uotes
commit
|
commitdiff
|
tree
2016-01-07
David
v
a
n der Spoe
l
Mad
e
normal modes work
with shel
l
s
an
d
v
s
ites
commit
|
commitdiff
|
tree
2015-11-24
David va
n
d
er Spo
e
l
Fixe
s
n
ewl
y
int
r
oduced bug in make
_
nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
Da
v
id van der Spoel
Mov
e
d do
m
d
ec st
r
u
ctures out of com
m
rec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Dav
i
d van der Spoel
Clea
n
ups i
n
le
g
acyhe
a
d
e
r/type
s
/
c
o
mmrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
Dav
i
d van der Spo
e
l
Me
r
g
e
d
l
e
gac
y
headers/types/qmmm
r
e
c
.
h
into mdlib/qm
m
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van der
S
p
oel
Mer
g
ed gen
b
or
n
.
h from legacyheaders/types
i
nto mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Spoel
Move
d
legacyheaders/type
s
/group
.
h to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der S
p
oel
Merged
l
egacyh
e
ader
s
/types/ns
.
h and nblis
t
.
h to
m
dt
y
pes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Spoel
Combine enums
.
h and
n
ames*
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der Spoel
Merge
d
l
egacyheaders/nrnb
.
h and typ
e
s
/
n
rnb
.
h to
gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
v
id van
d
er
S
p
oel
Moved mdatom
.
h
from lega
c
yheader/t
y
pes to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spo
e
l
Moved legacyheader
s
/types/energy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van de
r
Spoel
Merged legacyhead
e
rs/types/input
r
ec
.
h
into m
d
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Da
v
id
van der Spoel
Merged
legacyheaders/
t
ypes/state
.
h into
m
dtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van
d
er Sp
o
e
l
Replaced
a
tom_id
b
y int
.
commit
|
commitdiff
|
tree
2015-11-13
D
avid van der Spoel
M
o
ve
d
genborn
.
h to mdl
i
b
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved
t
xtdump
.
*
t
o fil
e
io
.
commit
|
commitdiff
|
tree
2015-11-12
David van
d
e
r
Spoel
Moved copyrite
.
* to fileio from gmx
l
ib and leg
a
cyheade
r
s
.
commit
|
commitdiff
|
tree
2015-11-11
David
van der Spoel
Moved inputrec
.
* fro
m
gmxlib and legacyheaders to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
D
avid van der
Spoel
Removed legacyheaders
/
typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Da
v
id van der Spoel
Moved df_hi
s
tory utility
r
outines from typede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der S
p
oel
R
e
placed N
O
TSET f
r
o
m type
d
e
f
s
.
h by lo
c
a
l s
o
lutio
n
s
.
commit
|
commitdiff
|
tree
2015-10-23
D
a
v
i
d van der Spoel
Removed energy
h
istory code
f
r
om
t
y
p
edefs to a s
e
para
t
e
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David v
a
n der Spo
e
l
Moved pbc
/
cut-of
f
relate
d
uti
l
i
tie
s
f
r
om
typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David
van der S
p
oel
Freed
memo
r
y
in l
e
ga
c
y stati
s
tics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David van der S
p
oel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed si
m
ple
.
h from nb_k
e
rnel_sse4_1
_
XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
Removed si
m
ple
.
h from nb_
k
ernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spo
e
l
Rem
o
v
ed simp
l
e
.
h
f
r
om
n
b_
k
e
r
nel_c
and nb_
k
ernel_sparc64_hp
c
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David
van der Spoel
Removed include
s
i
mpl
e
.
h from nb_kerne
l
_avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avi
d
van
d
er Spoel
Rem
o
v
ed simple
.
h from nb
_
kerne
l
_avx_2
5
6_XX
commit
|
commitdiff
|
tree
2015-10-02
D
av
i
d
va
n
d
er Spoel
R
e
m
o
ved
o
utpu
t
_env_t, no
w
using gmx
_
output_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
avid van
d
er Spoel
Removed
t
ypes/n
r
n
b
.
h from ty
p
edef
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoe
l
Removed types/nblist
.
h and types/nsgrid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van
der Spoel
Removed types/mdatom
.
h from ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
R
em
o
ved types/inpu
t
re
c
.
h
from typedefs
.
h and re
l
eted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
Fixes bug in the computat
i
o
n of
C
o
e
f
ficien
t
of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der S
p
oel
R
e
moved types/fo
r
cer
e
c
.
h from
t
y
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der
S
poel
R
e
moved include of
type
s
/i
f
un
c
.
h from t
y
pe
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
i
d van der S
p
o
e
l
Removed four in
c
lud
e
s from leg
a
cyhead
e
r
s
/
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
avid van der Sp
o
e
l
Removed l
e
g
a
cyheader
s
/t
y
pes
/
comm
r
ec_fwd
.
h fr
o
m typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
Da
v
i
d van der Spoel
Moved cont
e
n
t
f
rom mdrun
.
h to separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
R
emoved
<sys
/
types
.
h
> and "types/constr
.
h" from
t
y
pedefs
commit
|
commitdiff
|
tree
2015-09-09
D
a
vid van der Spoel
Rem
o
v
ed filei
o
/trx
.
h
f
rom typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
D
a
vi
d
v
a
n
d
e
r Spoel
Moved funct
i
ons operating o
n
f
o
rc
e
rec to
s
epa
r
a
t
e hea
d
e
r
.
commit
|
commitdiff
|
tree
2015-08-28
David van
d
er Spoel
Added
e
nerg
y
(edr)
file type to Options
h
eaders
.
commit
|
commitdiff
|
tree
2015-08-28
David v
a
n
der Spoel
Add
e
d ad
d
itional
c
onstru
c
tor to Strin
g
St
r
eam class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
D
a
vid van
de
r
Spoel
M
a
de output f
r
om dumping neightbo
r
lists easier to re
a
d
.
commit
|
commitdiff
|
tree
2015-07-31
David van der Sp
o
e
l
Change i
n
itial para
m
eters for testing expfi
t
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoel
Code for checking xv
g
files in tes
t
utils
.
commit
|
commitdiff
|
tree
2015-04-17
David v
a
n d
e
r Spoel
Updat
e
d expon
e
ntial
fitting to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van d
e
r Sp
o
el
C
larified c
o
m
m
ents for
t
ime-dependent electric
f
ie
l
ds
.
commit
|
commitdiff
|
tree
2015-04-08
Da
v
id van de
r
Spoel
Fixed incorrect output of g
b
_algorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
Da
v
i
d
van de
r
Sp
o
el
Updated documentation
f
or electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
D
a
v
id van
d
er Spoel
Four
n
ew quotes
f
r
om around the wor
l
d
.
commit
|
commitdiff
|
tree
2014-11-28
Da
v
id van der Spoel
Fixes recently introduce
d
bug in gmx ana
l
yze
.
commit
|
commitdiff
|
tree
2014-11-24
David van
d
er
Spoel
Added warnings fo
r
ewald-geom
e
try and surface-epsilon
commit
|
commitdiff
|
tree
next