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added mdp parameter for FE dH tables
2010-07-06
Be
r
k
Hess
add
e
d mdp par
a
meter for FE dH tables
commit
|
commitdiff
|
tree
2010-07-05
B
erk Hess
c
h
ange
d
the default maximum number of back
u
ps from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Be
r
k Hess
r
e
moved a l
o
t
of
slow FFT grid sizes from c
a
lc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
documented pull cosine weight
i
ng
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
r
enamed mdrun -cptnum to
-
c
pnum
commit
|
commitdiff
|
tree
2010-06-28
B
erk
H
es
s
a
d
d
ed mdrun -cpt
n
u
m
o
ption to keep and number
c
heckpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted ac
c
id
e
nti
a
l chang
e
of taba
n
gl
e
s in gro
m
pp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk He
s
s
a
dd
e
d include up
d
a
t
e
.
h to coupl
i
ng
.
c
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
added back cons
t
to gmx_sort c
o
mpare
p
aram
s
for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
removed obsolet
e
f
ftg
r
id code an
d
disabled
P
PPM
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
cha
n
ged pdb2gmx water model atom
c
ount detec
t
ion
commit
|
commitdiff
|
tree
2010-06-24
B
e
r
k
Hess
impl
e
mented
n
s
t
e
ps=-
1
for mdrun con
t
inuation a
n
d tp
b
c
onv
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk Hess
f
i
xed sm
a
l
l
oc
.
h
a
n
d sma
l
l
oc
.
c definition
i
nco
n
s
i
stencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge branch
'
ma
s
t
e
r
' of
git@git
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k Hess
removed statusi
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
B
erk Hess
fix
e
d
g
mx_eneconv com
p
i
l
er warn
i
n
g
s
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed eneconv -dt o
p
tion temporarily not writing averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
corr
e
cted edr
format is
s
ue introduced today
commit
|
commitdiff
|
tree
2010-06-21
Berk
H
es
s
a
d
d gmx_q
s
ort routine, since gli
b
c qsort is not
threadsaf
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
B
e
rk Hess
fixed typ
o
in fatal_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now md
r
un does
not
w
rite t
h
e trr file
w
hen i
t
would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
B
e
rk Hess
a
d
ded env var GMX_MAXBACKU
P
commit
|
commitdiff
|
tree
2010-06-17
Berk H
e
s
s
fi
x
for the previous mdrun
-
rerun commit
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hess
m
d
r
un -
r
erun
n
ow reads the rer
u
n traj
only on the ma
s
ter
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
minor update for previous replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
fixe
d
mdrun -rer
u
n giving
N
a
N w
i
th dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
a
dd
e
d water model sele
c
tion a
n
d lis
t
file to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
made
a separate
t
ips3p
.
i
tp
f
i
le
f
or CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk H
e
ss
Merge branc
h
'mast
e
r' of
git@git
.
gr
o
macs
.
o
rg:
g
r
o
macs
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
H
ess
ad
d
e
d
spc
e
to
c
harmm27
commit
|
commitdiff
|
tree
2010-06-16
Be
r
k
H
ess
fixe
d
MP
I
c
r
ash when
n
at_hom
e
=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
r
e
stored the old or
d
er
of
the mdrun option and remov
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
B
erk Hess
replaced more gm
x
_fatal
b
y collecti
v
e
c
a
lls in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
f
i
xed atom namin
g
i
n
encad c-termini
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
with nst
e
p
s
=-1
m
drun now prin
t
s ns/d
a
y
e
stima
t
e
commit
|
commitdiff
|
tree
2010-06-16
B
erk He
s
s
added nsteps=
-
1
option t
o
mdp
_
opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
ess
all en
e
rgy minimizers now d
o
0 steps with nsteps=
0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fixed
i
nco
r
r
e
ct
pdb2gmx CYS
2
to C
Y
S renaming which
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
allvsall
loops
no
w
trigger pa
r
t
i
cle d
e
composition
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
f
atal_
e
rror in
t
he
DD
initializat
i
on now calls MPI_Finalize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk Hess
a
dded -
c
w
d
option to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
Berk Hess
fixed mdrun counter res
e
t
tin
g
issues
commit
|
commitdiff
|
tree
2010-06-11
B
erk Hes
s
optimized
t
he number of th
r
eads
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
made DD work properly w
i
t
h all non-periodi
c
system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk He
s
s
added mo
r
e e
x
plana
t
i
o
n to idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk He
s
s
fi
x
ed unin
i
tializ
e
d variab
l
e in do_md
commit
|
commitdiff
|
tree
2010-06-10
Berk H
e
ss
f
i
xed particle decomp
o
sition
l
oad p
r
int
commit
|
commitdiff
|
tree
2010-06-04
Be
r
k Hess
fixed pdb2gmx messing up
coordinate
s
when deleting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk
H
e
s
s
added notes on mdp disre
pa
r
ame
t
ers
commit
|
commitdiff
|
tree
2010-06-03
Ber
k
H
e
s
s
distance rest
r
ain
t
ensemble
a
v
er
a
ging is n
o
longer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Be
r
k Hes
s
fixed b
u
g
in enum
p
a
rsing error
m
ess
a
ge
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
a
d
de
d
VV parameters to md
p
_opt
.
h
tml
commit
|
commitdiff
|
tree
2010-06-02
Berk
H
ess
f
i
xed more
G
r
omos at
o
m ty
p
e
name
c
a
s
es
commit
|
commitdiff
|
tree
2010-06-01
Be
r
k Hes
s
c
l
eaner fix for atom type case iss
u
e w
i
th GB parameters
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixed atom type case
issue
w
ith
GB parame
t
ers
commit
|
commitdiff
|
tree
2010-06-01
Berk
He
s
s
fixed two
G
B
bugs
commit
|
commitdiff
|
tree
2010-05-19
Berk Hess
f
i
xed md
r
un unwa
n
tingly mod
i
fying nst
e
nergy and nstlog
commit
|
commitdiff
|
tree
2010-05-18
Berk Hess
implement SSE
exp calc
u
l
ation for sol
v
e_pme
commit
|
commitdiff
|
tree
2010-05-17
Berk Hess
fixed so
m
e genborn incl
u
de file detai
l
s
commit
|
commitdiff
|
tree
2010-05-17
B
erk
H
ess
r
eo
r
der
e
d pm
e
_solve_yz
x
arguments
commit
|
commitdiff
|
tree
2010-05-14
B
e
rk Hess
minor pme_solve virial optimization
commit
|
commitdiff
|
tree
2010-05-14
Berk Hes
s
fi
x
e
d segv with m
d
run -n
p
me 1
commit
|
commitdiff
|
tree
2010-05-12
B
erk
H
ess
fix
e
d case of atom type
s
i
n
the Gromos force fi
e
lds
commit
|
commitdiff
|
tree
2010-05-12
B
e
rk Hess
corrected pdb2gmx fo
r
ce field
comments
commit
|
commitdiff
|
tree
2010-05-11
Berk He
s
s
ma
d
e
atom
ty
p
es case sen
s
it
i
v
e
commit
|
commitdiff
|
tree
2010-05-11
Berk
Hes
s
fixed b
u
g in pdb2gmx h
d
b i
n
itial
i
za
t
ion
commit
|
commitdiff
|
tree
2010-05-11
Berk He
s
s
a
d
ded
p
roper DNA and
RNA
r
esidue re
c
og
n
ition
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
ad
d
ed pr
o
per DNA a
n
d
RNA residue recog
n
ition
commit
|
commitdiff
|
tree
2010-05-11
Berk He
s
s
f
ixed incorrect pdb2gmx res
i
due name matc
h
ing
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
fixed bug with
p
db2gmx and
multiple
r
tp files
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
added
c
h
eck for sys/
t
ime
.
h existence
commit
|
commitdiff
|
tree
2010-05-11
B
erk Hess
updated and f
i
ne-tuned the coeff
i
cie
n
ts for the PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
removed in
c
lude of
complex
.
h
i
n fft5d
.
h
commit
|
commitdiff
|
tree
2010-05-10
Berk
H
ess
fi
x
ed underall
o
cation in
gmx_fft_
i
n
i
t_many_1d_real
commit
|
commitdiff
|
tree
2010-05-10
B
e
r
k Hes
s
fi
x
ed nam
e
in gro
m
o
s
43a1
.
ff Makefi
l
e
.
am
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
moved alc
o
hol files from top t
o
the
for
c
e field subdirectories
commit
|
commitdiff
|
tree
2010-05-10
Berk H
e
s
s
moved alcohol fi
l
es
f
r
om t
o
p to the
fo
r
ce field subdirec
t
ories
commit
|
commitdiff
|
tree
2010-05-10
Berk
H
e
s
s
com
p
letion of the pdb2gm
x
re
s
idue renaming chan
g
e
commit
|
commitdiff
|
tree
2010-05-07
Berk
Hess
changed inter
n
al Gromacs naming of
c
y
s, his and l
y
s
commit
|
commitdiff
|
tree
2010-05-07
Berk He
s
s
ad
d
ed a column for single
residue
chain to r
2
b
f
ile
commit
|
commitdiff
|
tree
2010-05-07
Berk
H
ess
fixed se
g
v
i
n
grompp when g
m
xcpp reports
a
n e
r
ror
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
m
a
d
e
gromp
p
charg
e
warn
i
ng less s
e
n
sitive to rounding
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
made PME ene
r
gy
an
d
vi
r
i
al calculatio
n
o
ptional
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
M
er
g
e com
m
it '
o
rigin/
2
dpm
e
'
commit
|
commitdiff
|
tree
2010-05-07
B
e
rk He
s
s
removed solve_
x
yz
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
nst
e
n
e
r
gy
is now
-
1
by
d
e
fa
u
lt, meanin
g
nstl
i
st
commit
|
commitdiff
|
tree
2010-05-06
Berk Hess
f
i
xed some details
for
n
stcalcenergy>1
commit
|
commitdiff
|
tree
2010-05-04
Berk H
e
ss
fi
x
ed com
p
iler
war
n
i
ng
commit
|
commitdiff
|
tree
2010-05-03
B
erk Hess
r
e
moved incorr
e
ct P
M
E grid factor check
commit
|
commitdiff
|
tree
2010-05-03
Berk Hess
added so
m
e explanati
o
n
commit
|
commitdiff
|
tree
2010-04-30
Berk Hess
Merge commit 'ori
g
in/master' into 2dpme
commit
|
commitdiff
|
tree
2010-04-30
B
e
rk Hess
correcte
d
pm
e
gather f
l
op
c
oun
t
f
r
om 12 to 6
commit
|
commitdiff
|
tree
2010-04-30
Ber
k
H
ess
fixed rest cycl
e
count in seria
l
commit
|
commitdiff
|
tree
2010-04-30
Berk
H
e
s
s
f
ixed multiple print of run t
e
rmi
n
ation messag
e
commit
|
commitdiff
|
tree
2010-04-30
B
er
k
Hess
fixed segv in energy file rea
d
ing
commit
|
commitdiff
|
tree
2010-04-29
Berk
H
e
s
s
Merg
e
commit 'origin/master' into
2dpme
commit
|
commitdiff
|
tree
2010-04-29
Berk Hess
changed
the PME particle
c
ommunicat
i
on buffer
region
.
.
.
commit
|
commitdiff
|
tree
2010-04-29
B
e
rk H
e
ss
fi
x
ed posres allocation issue
commit
|
commitdiff
|
tree
2010-04-29
Berk Hess
fixed par
t
icles
o
ut of PME node cra
s
h w
i
th 2D PME
commit
|
commitdiff
|
tree
2010-04-28
Berk Hess
fi
x
ed
t
h
e
g
rompp -e op
t
ion and added notes on
checkpoint
.
.
.
commit
|
commitdiff
|
tree
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