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Couple of new quotes
2016-07-11
M
i
c
h
a
el Sh
i
rts
Fix for in
c
or
r
ectly
setting expanded en
s
e
mble when
.
.
.
commit
|
commitdiff
|
tree
2016-01-07
Michael Shirts
Fixes two problem
s
r
ela
t
ed to restar
t
s for vv
.
commit
|
commitdiff
|
tree
2015-10-12
Michael S
h
irt
s
Fix for l
a
ck
of
COM
removal for md-vv
commit
|
commitdiff
|
tree
2015-08-18
Michael
S
hirts
F
ix for expanded
e
nsemble
.
commit
|
commitdiff
|
tree
2015-04-30
Mic
h
ael Shirts
Fix
f
o
r
r
arely occuring replica exchang
e
er
r
or
.
commit
|
commitdiff
|
tree
2014-06-29
Mic
h
ael
Shirts
A
l
low p
r
inting potent
i
al
e
nergi
e
s to dhdl
.
xvg fil
e
commit
|
commitdiff
|
tree
2014-04-21
M
i
c
h
ael Shi
r
ts
Issue warnings for
p
o
tenti
a
l s
w
itc
h
w/o d
e
finin
g
switch
.
.
.
commit
|
commitdiff
|
tree
2014-02-26
Mic
h
ael Shirts
Up
d
ating and improving
An
d
ersen the
r
mostat do
c
u
mentat
i
on
commit
|
commitdiff
|
tree
2014-02-06
Michael S
h
irts
EE dhd
l
header sho
u
ld no
t
spe
c
i
fy one la
m
bda
commit
|
commitdiff
|
tree
2013-10-17
Michael Sh
i
rts
Restarting from che
c
kpoint no longer rei
n
itializes
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
M
i
chael Shirt
s
turning o
f
f
expanded e
n
s
e
m
ble for all
i
ntegrators but
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
M
i
chael Shirts
Fixes a problem with pair type 2
i
n
teractions with
.
.
.
commit
|
commitdiff
|
tree
2013-09-26
Micha
e
l
S
h
irts
log
i
c fix for f
r
ee e
n
ergies with mdrun -rerun
commit
|
commitdiff
|
tree
2013-09-16
Michael Shirts
Fixing
manual for sc-coul
d
escription
.
commit
|
commitdiff
|
tree
2013-08-02
Mic
h
a
el Shirts
Fixing prob
l
em caused
by o
v
erflow in expanded ensemble
.
commit
|
commitdiff
|
tree
2013-06-20
Mic
h
ael Shirts
F
i
x
i
ng a problem when
d
hdl and replex
a
r
e n
o
t mul
t
iples
commit
|
commitdiff
|
tree
2013-05-30
Michael S
h
i
r
ts
Fixing the co
n
straint
dhdl
t
e
rm in
shake
commit
|
commitdiff
|
tree
2013-05-26
Michael Shirts
Fix of me
m
o
ry lea
k
commit
|
commitdiff
|
tree
2013-05-21
Mic
h
ael Shi
r
ts
Fixed pro
b
lem w
i
th bond constraint dh
d
l being left
out
commit
|
commitdiff
|
tree
2013-05-08
Michael Shirt
s
f
i
xin
g
rerun wit
h
free ene
r
gy +
.
xtc or
.
gro
commit
|
commitdiff
|
tree
2013-04-30
Michael
S
hirt
s
F
i
x
ing ha
n
dling of p
e
rtur
b
ation mass
c
h
a
nges
.
commit
|
commitdiff
|
tree
2013-04-26
Michael
S
hirts
Fixin
g
a problem
w
i
t
h dh/dl 1-4 interaction
s
commit
|
commitdiff
|
tree
2013-02-25
Michael Shirts
fix imcompatibility with tpr vers<64
wi
t
h f
r
ee en
e
r
gy
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
M
i
chael
Shirts
bugfix for md-vv
+
n
ose-hoover + (nstcalce
n
ergy >
nsttco
u
p
le)
commit
|
commitdiff
|
tree
2013-01-18
Micha
e
l
Shirts
Addendum for expanded ens
e
mble
optio
n
s plus for
m
atting
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Micha
e
l Shirts
fixes issu
e
s
with pressure control and infrequent e
v
a
luation
commit
|
commitdiff
|
tree
2013-01-15
Mich
a
e
l
Shir
t
s
C
o
ntinuation of documentation
f
or expanded ensemble
.
commit
|
commitdiff
|
tree
2013-01-13
Michae
l
Shirt
s
Fixes for
m
d-vv and rerun
commit
|
commitdiff
|
tree
2013-01-01
Mich
a
e
l
Shi
r
t
s
Fixed a bug that w
i
t
h multip
l
e
exchang
e
s
commit
|
commitdiff
|
tree
2012-12-20
Michael Sh
i
rts
Fixes
f
or a
n
ders
e
n
t
e
m
p
erature
c
ontrol
commit
|
commitdiff
|
tree
2012-12-20
Michael S
h
i
r
ts
Fi
x
e
s for expanded
e
nsembl
e
a
n
d HREPEX
commit
|
commitdiff
|
tree
2012-12-20
Michae
l
Shirts
Fix for t
h
e p
r
essu
r
e
in MTTK
w
ith constraints
+
dispersion
commit
|
commitdiff
|
tree
2012-12-14
Michae
l
Shirts
F
ix
e
s re
d
mine
issue #1071
commit
|
commitdiff
|
tree
2012-12-06
Micha
e
l Shirts
Remo
v
ing (inaccurate) virial
temperatu
r
e
c
alc
.
commit
|
commitdiff
|
tree
2012-11-27
Michael Shirts
Remov
e
s memory allocation
from free e
n
ergy fo
r
eign
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Michael S
h
irts
C
larification of mdp_opt, ad
d
nstexpand
d
efau
l
ts &
.
.
.
commit
|
commitdiff
|
tree
2012-10-12
Michael Shirts
Fixing
i
s
sues with re
p
l
ica exchan
g
e
commit
|
commitdiff
|
tree
2012-07-31
Michael Shi
r
ts
Ad
d
ed a check for efep that was miss
i
ng
.
commit
|
commitdiff
|
tree
2012-07-29
Micha
e
l S
h
ir
t
s
F
i
x
i
n
wh
e
n
to call th
e
constraints for
a
nderse
n
.
commit
|
commitdiff
|
tree
2012-06-29
Mi
c
h
a
el Shirts
M
inor
f
ormatting and co
n
sistency changes to tx
t
du
m
p
.
c
commit
|
commitdiff
|
tree
2012-06-29
Michael Shi
r
ts
Co
r
recte
d
checkpoin
t
ver
s
ion issu
e
s
w
ith free energy
.
.
.
commit
|
commitdiff
|
tree
2012-06-24
Michael Shirts
Merge
"
F
ix
m
dp_opt formatting of expanded ensemble
.
.
.
commit
|
commitdiff
|
tree
2012-06-04
Mi
c
hael
S
hirts
M
e
rging in fre
e
energy
,
exp
.
ensemble, & ande
r
sen t
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
Michael
Shirts
F
i
x
e
s
problems with g_
m
sd and
g
_energy
commit
|
commitdiff
|
tree
2011-09-05
M
i
c
h
ael
S
hirts
Merge "fixed
i
ncorr
e
ct p
V
te
r
m i
n
the energy file"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Mich
a
el S
h
irts
number o
f
degrees
o
f fre
e
dom
c
a
n be fra
c
tional --
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael S
h
ir
t
s
Additional fixes to the ns
t
tc
o
uple and nstpcou
p
le worki
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael Shi
r
t
s
Additional changes
f
or setting nst
t
c
oup
l
e
commit
|
commitdiff
|
tree
2010-08-19
Michae
l
Shirts
F
i
x f
o
r
r
ead
i
r
.
c
so that nstpcouple
a
nd nsttcoup
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mich
a
e
l Shir
t
s
Fixe
d
b
u
g
wit
h
md-vv
a
nd with v-rescale
commit
|
commitdiff
|
tree
2010-08-19
Michael Shir
t
s
Proposed fix
for v-rescale and
b
erendsen for veloci
t
y
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
M
i
chael Shirts
Merge b
r
anch 'r
e
lease-4-5-patches' of g
i
t@
g
it
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael S
h
irts
Merge
b
r
a
nch 'release-4-5-patches' of git
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirt
s
Merg
e
br
a
n
c
h
'relea
s
e-4-5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Micha
e
l Shirts
Change
d
the way energy c
o
nservation b
o
okeeping is done
.
commit
|
commitdiff
|
tree
2010-08-17
Michael Shirts
Merge branch 're
l
ease
-
4-5-pa
t
ches' o
f
git@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Michael Sh
i
rts
Tryin
g
to ge
t
vscale
w
o
rking wi
t
h
vv
.
commit
|
commitdiff
|
tree
2010-08-09
Mi
c
h
ael Shirts
First pass at getting VV
/ v-rescale
f
o
rmula c
o
rrect
.
commit
|
commitdiff
|
tree
2010-08-07
Michael Shirts
Eliminated so
m
e
commen
t
ed out
cod
e
.
commit
|
commitdiff
|
tree
2010-07-11
Mi
c
hael
Shirts
Fixed initial di
s
pla
y
of
t
emperat
u
re
f
o
r
md-vv-avek
commit
|
commitdiff
|
tree
2010-07-10
Mic
h
ael Shirts
Removed
c++ style
c
omme
n
t
.
commit
|
commitdiff
|
tree
2010-07-10
Mic
h
ael
Shirts
Fixed
mi
n
or formatti
n
g
c
o
n
flict
.
commit
|
commitdiff
|
tree
2010-07-10
Mich
a
el
Shirts
Fixing
the
i
nclude fi
l
e definition for trotter_
u
pda
t
e
.
commit
|
commitdiff
|
tree
2010-06-27
Michael
Shi
r
ts
Merge
br
a
nch 'master' of
g
it@git
.
gro
m
a
cs
.
or
g
:
g
romacs
commit
|
commitdiff
|
tree
2010-06-27
Mi
c
h
ael Shirts
Fixed
g
mx_membed
.
c to ag
r
ee with domd
.
c
commit
|
commitdiff
|
tree
2010-06-27
M
i
chael S
h
irts
Restored the forb
i
dding of n
s
tcalcenergy for vv
for
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Michael Shirts
*Started to
a
dd support of nstcalcene
r
gy
t
o vv versions
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Mich
a
el Shirts
Har
d
ed the shake constraint package so tha
t
it
couldn
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
Merge b
r
anch
'
mas
t
e
r
' of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
Elimina
t
ing the
nstcalc issue
wit
h
vv -
-
it sh
o
uld
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
add
e
d more info
r
mation in
mdp
options
.
commit
|
commitdiff
|
tree
2010-06-12
Michael Sh
i
r
t
s
Raised the NHC
H
AINLENG
T
H defa
u
lt
t
o
10
commit
|
commitdiff
|
tree
2010-06-11
Michael
S
h
ir
t
s
Fixed various logic
problem
s
p
reventing proper energy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
Michael Shirt
s
ad
d
ed a secondary check for erro
r
if the error is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
M
ichael Shirts
Merge
branch
'm
a
ster' of git@git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-02-03
Mic
h
a
e
l
Shirts
F
i
x for me
m
ory error a
f
fecting
p
a
r
a
llel simul
a
tions
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mich
a
el Shirts
A fi
x
to
c
ompute_bonds_lambd
a
-
the value of nr
_
no
n
p
erturbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael Shirts
Revising the
i
terat
i
on of
NPT for single p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Fin
a
l fix for parallel checkpointing wi
t
h
Nose-ho
o
ver
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Continu
i
ng fixes
f
or checkpointing in parallel
(
a
l
so
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael
S
h
i
r
t
s
M
e
rge br
a
nch 'master' of git@git
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-22
Mi
c
hael Sh
i
rts
A
variety of changes to corr
e
c
tly
d
o
c
h
eckpoin
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shir
t
s
Removed warning cause
d
by thro
w
ing a
w
ay 'const' definitio
n
.
commit
|
commitdiff
|
tree
2010-01-18
Micha
e
l
Shirts
Fi
x
es
f
o
r entry to and rea
d
ing e
x
t
ended system v
a
riab
l
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shi
r
ts
Addin
g
ba
c
k in c
h
ange
s
that
m
ysteriously disappear
e
d
.
commit
|
commitdiff
|
tree
2010-01-17
Michae
l
Shirts
Revisions to ha
r
monize
ve
l
ocity verlet with B
e
rk'
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
M
i
chae
l
Shirts
F
i
xed
typo
in changi
n
g name of
n
nhchains
to nhch
a
inlen
g
th
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
removed a depend
e
ncy on a file that di
d
n
ot exist
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Shir
t
s
c
hanges the nnhchains
n
ame to nhchainl
e
n
g
th
commit
|
commitdiff
|
tree
2010-01-11
M
i
chael
Shi
r
ts
Merge branch 'master'
o
f g
i
t:/
/
git
.
gromacs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Mich
a
el Shir
t
s
Merge branch
'
m
aster'
o
f git://git
.
gromacs
.
org/gro
m
acs
commit
|
commitdiff
|
tree
2010-01-07
Mic
h
ael Shirts
Merge br
a
n
c
h 'master' of git://gi
t
.
gromacs
.
org
/
gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
C
ommented o
u
t
some
c
h
e
cking c
o
d
e
u
seful for the future
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shi
r
t
s
Removed some legacy "#if 0"
c
ode
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Merge b
r
an
c
h 'maste
r
' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-04
Micha
e
l Shir
t
s
Improved
output
i
n
mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
No l
o
nger
need to specify f
e
p-lambda every t
i
me --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hael Shirts
fixe
s
for handl
i
ng periodicity f
o
r dih
e
dra
l
re
s
t
r
a
in
t
s
.
commit
|
commitdiff
|
tree
2010-01-03
Mic
h
a
e
l Shirts
re
m
oved
cod
e
that had been #ifdef'ed out
.
commit
|
commitdiff
|
tree
2010-01-03
Micha
e
l S
h
ir
t
s
Fixe
d
the is
s
ues with the restraint calcul
a
tion
s
.
commit
|
commitdiff
|
tree
next