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Misc. Doxygen build system improvements
2014-02-26
M
ich
a
el Shirts
Updating and improvin
g
And
e
r
sen
therm
o
s
tat docume
n
ta
t
ion
commit
|
commitdiff
|
tree
2014-02-06
M
ic
h
ael S
h
irts
EE dhdl
h
eader
should not specify one lambd
a
commit
|
commitdiff
|
tree
2013-10-17
Michael Shirts
Restarti
n
g from
checkpoint no lon
g
er
r
e
initializes
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirts
turnin
g
off expanded
ensemble fo
r
a
l
l
i
ntegrat
o
rs but
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirt
s
Fixe
s
a pr
o
blem with pair t
y
pe 2
interac
t
i
o
ns with
.
.
.
commit
|
commitdiff
|
tree
2013-09-26
Michae
l
Shi
r
ts
l
o
gic fix for fr
e
e
e
nergies with
mdr
u
n
-
rerun
commit
|
commitdiff
|
tree
2013-09-16
Michael S
h
irts
F
i
xing manual for sc-
c
oul des
c
ription
.
commit
|
commitdiff
|
tree
2013-08-02
M
i
chael
Shi
r
ts
Fixing problem caused
b
y overflow in
e
x
panded ensembl
e
.
commit
|
commitdiff
|
tree
2013-06-20
Michael Shirts
Fixin
g
a
p
roble
m
w
h
en dhdl
a
nd replex are no
t
m
u
ltiples
commit
|
commitdiff
|
tree
2013-05-30
M
i
c
h
a
el Shirt
s
Fixing the constraint dhdl term i
n
shake
commit
|
commitdiff
|
tree
2013-05-26
M
i
chael Shirts
Fix of memory leak
commit
|
commitdiff
|
tree
2013-05-21
M
ichael
Shirts
Fixed
problem
w
ith bond constraint dhdl being
l
eft out
commit
|
commitdiff
|
tree
2013-05-08
Michae
l
Shirts
fix
i
ng
r
eru
n
with free energ
y
+
.
x
tc or
.
gro
commit
|
commitdiff
|
tree
2013-04-30
Michael Shirts
Fix
i
ng handlin
g
of
pertur
b
ation ma
s
s changes
.
commit
|
commitdiff
|
tree
2013-04-26
Michael Shirts
Fixing a
p
roblem
with d
h
/dl 1-
4
i
nte
r
acti
o
n
s
commit
|
commitdiff
|
tree
2013-02-25
Michael
S
h
irts
fix imcompatibility with tpr vers<64 with
free energy
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Mi
c
hae
l
S
hir
t
s
bugfix for md-vv + nose-hoov
e
r
+ (
n
stcalce
n
ergy
>
ns
t
tcouple)
commit
|
commitdiff
|
tree
2013-01-18
Michael Shirts
Addendum f
o
r ex
p
anded ensembl
e
options plus forma
t
t
ing
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Micha
e
l Shirts
fixe
s
issu
e
s
with
p
res
s
u
r
e
c
o
n
t
rol and infr
e
q
u
ent eval
u
ation
commit
|
commitdiff
|
tree
2013-01-15
Michael Shi
r
ts
Continuati
o
n
of doc
u
menta
t
ion for expanded ensemble
.
commit
|
commitdiff
|
tree
2013-01-13
Micha
e
l Shirts
Fixes for md
-
vv and reru
n
commit
|
commitdiff
|
tree
2013-01-01
Michae
l
Shirts
Fixed
a b
u
g that with m
u
ltiple e
x
changes
commit
|
commitdiff
|
tree
2012-12-20
Michael Shirts
Fixes
f
or a
n
dersen t
e
mperature
control
commit
|
commitdiff
|
tree
2012-12-20
Michael Shirts
Fixes for
exp
a
nded
e
n
semble
and
H
REPEX
commit
|
commitdiff
|
tree
2012-12-20
Michae
l
S
h
ir
t
s
Fix for the pressure in MTTK with constrai
n
t
s
+ dispersion
commit
|
commitdiff
|
tree
2012-12-14
M
i
c
hael Shi
r
ts
Fixes re
d
mine iss
u
e #10
7
1
commit
|
commitdiff
|
tree
2012-12-06
M
i
chael Shirts
Removing (inaccurate
)
vi
r
ia
l
tempera
t
ure calc
.
commit
|
commitdiff
|
tree
2012-11-27
M
i
chael Shirts
Removes memory allocation fr
o
m
free energ
y
foreign
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Michael Shirts
Clari
f
ication
o
f m
d
p_opt, a
d
d n
s
texp
a
nd default
s
&
.
.
.
commit
|
commitdiff
|
tree
2012-10-12
Michael
S
hirts
Fixing issues with replica exchange
commit
|
commitdiff
|
tree
2012-07-31
Mi
c
h
a
el S
h
irts
Adde
d
a
check
f
o
r efep that was missing
.
commit
|
commitdiff
|
tree
2012-07-29
Micha
e
l Shirts
F
ix in
w
hen to c
a
ll the constraints for anders
e
n
.
commit
|
commitdiff
|
tree
2012-06-29
Michael
S
hirts
M
inor formatt
i
ng and co
n
sistenc
y
changes
t
o
tx
t
dump
.
c
commit
|
commitdiff
|
tree
2012-06-29
Mic
h
ael Shir
t
s
Cor
r
e
c
ted
c
h
eckpo
i
nt ver
s
ion
i
s
sue
s
with free energy
.
.
.
commit
|
commitdiff
|
tree
2012-06-24
Michael Shirts
M
e
rge "Fix mdp_opt formatting of expanded ensemble
.
.
.
commit
|
commitdiff
|
tree
2012-06-04
Michael Shir
t
s
Mergi
n
g in free energy, exp
.
e
nse
m
ble,
& ande
r
sen t
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
Michael S
h
irts
F
i
xes problems
w
ith g
_
msd an
d
g_en
e
rgy
commit
|
commitdiff
|
tree
2011-09-05
Michael Shirt
s
Merge "fixed
i
ncorr
e
ct
pV ter
m
in the energy f
i
le"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Michael Shi
r
t
s
number o
f
degrees o
f
fre
e
dom ca
n
be fractional
-- in
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mich
a
el Shirts
Add
i
tion
a
l fixes to the nsttcouple
and nstpcouple working
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael Shirt
s
Addition
a
l ch
a
n
ges
f
or
s
e
tting nsttcoupl
e
commit
|
commitdiff
|
tree
2010-08-19
Michael
S
hirts
F
i
x for
r
e
a
d
i
r
.
c so
that
n
stpcou
p
le and nst
t
c
o
u
ple
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mi
c
hael Shirts
Fixed bug with md-vv and with v-rescale
commit
|
commitdiff
|
tree
2010-08-19
Michael
S
hirts
P
roposed fix
f
or v-
r
escale and berendsen for ve
l
ocity
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michae
l
S
h
irts
Mer
g
e b
r
anch 'release-4-5-patch
e
s' of
g
it@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Mich
a
el Shirts
Merge branch 're
l
ease-4-5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Mi
c
hael Shirts
Me
r
g
e branch 'release-4-5-patches' of git@git
.
gr
o
mac
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
M
ichael S
h
irts
Changed
t
he
w
ay
e
nergy conservation
bookee
p
ing is done
.
commit
|
commitdiff
|
tree
2010-08-17
Michael Shirts
Merge branc
h
'release
-
4
-5-patches' o
f
git@git
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Michael Shirt
s
Trying to
g
et vscal
e
wo
r
king with vv
.
commit
|
commitdiff
|
tree
2010-08-09
Michael S
h
ir
t
s
Firs
t
pass at getting V
V
/ v
-
r
e
scale formula co
r
rect
.
commit
|
commitdiff
|
tree
2010-08-07
Mi
c
hae
l
Sh
i
rt
s
E
lim
i
n
ate
d
some commented out code
.
commit
|
commitdiff
|
tree
2010-07-11
Mich
a
e
l Shirts
Fixed initial dis
p
lay of temperat
u
re for
m
d-vv-av
e
k
commit
|
commitdiff
|
tree
2010-07-10
M
ichae
l
Shirts
Removed c++
s
tyle comment
.
commit
|
commitdiff
|
tree
2010-07-10
Michae
l
Shirts
Fi
x
ed minor f
o
rmatting confli
c
t
.
commit
|
commitdiff
|
tree
2010-07-10
Mic
h
ael Shirts
Fixing the includ
e
file definition fo
r
tr
o
tte
r
_update
.
commit
|
commitdiff
|
tree
2010-06-27
M
i
chael Sh
i
rts
Merg
e
b
r
anch 'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-27
Micha
e
l Shirts
Fixed gmx_mem
b
e
d
.
c to agree
with domd
.
c
commit
|
commitdiff
|
tree
2010-06-27
Michae
l
S
hirts
Restored th
e
forbi
d
ding
o
f n
s
tcalce
n
ergy for vv for
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
M
ichael Shirts
*Started to ad
d
support of nstcal
c
energy to vv v
e
rsions
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Michael
S
hirts
Harded the shake con
s
tr
a
int p
a
ckage so that it coul
d
n
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Mi
c
hae
l
Shir
t
s
Merg
e
branch 'm
a
s
ter' of git@git
.
gro
m
acs
.
org:gr
o
m
acs
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
El
i
minating the nstcalc issue
w
i
t
h vv -- it
shou
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Mich
a
e
l Shirts
added more information in mdp option
s
.
commit
|
commitdiff
|
tree
2010-06-12
Michael Sh
i
rts
Raised t
h
e
N
HCHAINLE
N
GT
H
default to
10
commit
|
commitdiff
|
tree
2010-06-11
Michae
l
Shirts
Fixed variou
s
l
og
i
c problems preventing proper
e
nergy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
Michael Shirts
added a seco
n
d
a
ry
c
heck
for error if
t
he error
is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Michae
l
Shir
t
s
Merge
b
ranch
'
master' of g
i
t@gi
t
.
grom
a
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-02-03
Michael Shirts
Fix for memory error affecting pa
r
a
llel s
i
mu
l
atio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael Shirts
A fix to compute
_
bonds_lam
b
da
- the va
l
u
e
of n
r
_nonp
e
rturbe
d
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
M
i
chael S
h
irts
Re
v
is
i
ng
t
he it
e
rati
o
n of NPT for single precision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Mich
a
el
Sh
i
rts
Final fi
x
f
o
r
parallel checkpointin
g
wit
h
Nose-ho
o
ver
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Con
t
inuing fixes for checkpointing
i
n pa
r
allel (also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michae
l
Sh
i
r
ts
M
e
rge
b
ranch
'
master' of g
i
t@git
.
gromacs
.
o
rg:grom
a
cs
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
A variety o
f
chan
g
es t
o
co
r
rec
t
ly do che
c
k
p
ointing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
M
i
chael Shir
t
s
Remove
d
warning caused
by t
h
ro
w
ing away 'con
s
t' definition
.
commit
|
commitdiff
|
tree
2010-01-18
Michael S
h
irts
Fixes for entry
t
o and reading
e
xten
d
ed syste
m
varia
b
les
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shirts
A
d
ding back in ch
a
n
ges that
m
y
s
teriousl
y
d
i
s
a
p
p
eared
.
commit
|
commitdiff
|
tree
2010-01-17
Michae
l
Shir
t
s
Re
v
isions to harmonize
v
el
o
city verlet wi
t
h
B
erk's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
Fixed typo
i
n chan
g
ing name of nnhchains to nhchainlength
.
commit
|
commitdiff
|
tree
2010-01-11
Mi
c
hael Shi
r
ts
remo
v
ed a depen
d
en
c
y on a f
i
le
that did
n
o
t
exist
.
commit
|
commitdiff
|
tree
2010-01-11
Michae
l
Shirts
cha
n
ges the nnh
c
hains name to nhchainleng
t
h
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
Merge branch 'master' of git://git
.
gromacs
.
org/gromac
s
commit
|
commitdiff
|
tree
2010-01-07
Michael S
h
irts
Merg
e
branc
h
'master'
o
f git:
/
/git
.
gromacs
.
o
r
g/gr
o
m
acs
commit
|
commitdiff
|
tree
2010-01-07
Michael S
h
irt
s
Merge bran
c
h 'mas
t
er' of git://
g
it
.
gr
o
macs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Commented out
some checking code useful for
t
h
e
future
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
M
i
chael
Shirts
Removed some legacy "#
i
f 0" code
.
commit
|
commitdiff
|
tree
2010-01-04
M
i
chael Sh
i
rts
Me
r
ge b
r
anch 'ma
s
ter' of git@git
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael
Shir
t
s
Improved outp
u
t in
m
debin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michae
l
Shirts
No longer
n
ee
d
t
o
specify f
e
p-lambda eve
r
y
t
ime
-
-
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
fix
e
s
f
o
r handling p
e
rio
d
i
c
i
ty
f
or
d
ihedral restraints
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hae
l
S
h
irts
rem
o
ve
d
code t
h
at ha
d
been #ifdef'e
d
out
.
commit
|
commitdiff
|
tree
2010-01-03
Michae
l
Shir
t
s
Fixed the issue
s
w
i
th the restraint cal
c
ulations
.
commit
|
commitdiff
|
tree
2010-01-02
Michael Shirts
R
e
vision
o
f
handling of for
e
ign lambda
b
o
n
ds
.
commit
|
commitdiff
|
tree
2010-01-01
Micha
e
l Shirts
Fix for nonb
o
ndeds
.
commit
|
commitdiff
|
tree
2010-01-01
Michael
S
hirts
More fixe
s
fo
r
the multicomponent l
a
mbda
.
commit
|
commitdiff
|
tree
2010-01-01
Michael Shirts
Latest revision of
f
r
e
e energy changes
.
commit
|
commitdiff
|
tree
2009-12-29
M
i
chae
l
S
hirts
F
re
e
energy now
apparently working wi
t
h multilambda
.
commit
|
commitdiff
|
tree
2009-12-27
Michael Shir
t
s
M
erge bra
n
ch 'master' of
g
i
t
@git
.
g
romac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-27
Mic
h
ael
Shirts
Merge branc
h
'master'
of
git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
next