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fixed zero viscosity energy/log file output with cos_acceleration
2011-01-10
Be
r
k
Hess
f
ixed zero v
i
scosity energy/log fil
e
output wit
h
cos_acce
l
er
.
.
.
commit
|
commitdiff
|
tree
2011-01-04
Berk
H
e
ss
fixed grompp
l
ooking for inclu
d
e files in double relati
v
e
.
.
.
commit
|
commitdiff
|
tree
2010-12-22
Berk He
s
s
removed incorrect cit
a
t
i
on pr
i
nt of Engin2010 for pull
.
.
.
commit
|
commitdiff
|
tree
2010-12-21
B
e
rk Hess
pme
.
c work-
a
r
ound for MPI fatal error in pme
with parttic
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-12-16
B
e
r
k
H
ess
fixed in
c
orr
e
ct LJ table
i
n mdrun with rep
p
ow!=12
commit
|
commitdiff
|
tree
2010-12-16
Be
r
k Hess
removed
e
ditco
n
f warning
o
n bo
x
distance w
i
th -bt
commit
|
commitdiff
|
tree
2010-12-13
Berk He
s
s
fi
x
ed tpb
c
onv time options l
e
a
d
ing to
n
egativ
e
nsteps
.
.
.
commit
|
commitdiff
|
tree
2010-11-24
Berk Hess
fixed segv i
n
g
rompp
d
ue to gmxcp
p
n
ot checking fo
r
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Berk Hess
added
-resnr
optio
n
to editco
n
f
commit
|
commitdiff
|
tree
2010-11-09
B
erk Hess
fixed compil
e
r warning
in pdb2gmx
.
c
commit
|
commitdiff
|
tree
2010-11-05
Berk Hess
pdb2gmx now put
s
atoms with cgnr=-1
in se
p
arate charge
.
.
.
commit
|
commitdiff
|
tree
2010-11-04
Berk Hess
Fixed
md
.
log being opene
d
twice when a
p
p
ending,
wh
i
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Berk Hess
fixed incorrect
p
rint in f
a
ta
l
error on cha
r
ge group
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Berk Hess
proper
defi
n
e
d o
f
MAX_CH
A
R
GEGROUP_SIZE=32 in a s
i
ngle
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
Berk Hess
ad
d
e
d
HEM to HEME renami
n
g
f
or G
r
o
m
o
s
and Charm
m
f
f
's
commit
|
commitdiff
|
tree
2010-10-28
B
erk Hess
fixe
d
pd
b
2gmx chain
me
r
ging bug (
b
ugzilla 544)
commit
|
commitdiff
|
tree
2010-10-26
Berk Hess
fixed cycle pri
n
t type cast issue on certain platf
o
rms
.
.
.
commit
|
commitdiff
|
tree
2010-10-21
Berk He
s
s
clarified
m
ake
_
ndx
e
rror me
s
sage
commit
|
commitdiff
|
tree
2010-10-19
Berk Hess
change
d
enxio warn
i
ng into
f
at
a
l errors by de
f
a
ult
.
.
.
commit
|
commitdiff
|
tree
2010-10-18
Ber
k
Hess
fixed atom ty
p
e name ca
s
e f
o
r m
e
thanol
.
itp in g
r
omos43a1
.
ff
commit
|
commitdiff
|
tree
2010-10-18
Be
r
k Hess
fixed
possib
l
e ove
r
flow of unused variable in lincs
commit
|
commitdiff
|
tree
2010-10-18
Berk Hess
added checks for rar
e
e
vents that would make variables
.
.
.
commit
|
commitdiff
|
tree
2010-10-15
Berk Hes
s
more fi
x
es for TPI
wi
t
h
PME, now really fixed bugzi
l
la 590
commit
|
commitdiff
|
tree
2010-10-13
Berk Hess
fixed g_velacc -m not auto
m
atically usi
n
g
-s
commit
|
commitdiff
|
tree
2010-10-12
B
e
rk He
s
s
add
e
d n
o
t
e to g_density for us
i
ng g_energy for normal
.
.
.
commit
|
commitdiff
|
tree
2010-10-12
Be
r
k
Hess
fi
x
e
d inc
o
rrect d
i
spe
r
sion correction for TPI with
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
Berk
H
ess
f
i
xed typo in checkpoint warni
n
g
commit
|
commitdiff
|
tree
2010-10-08
Berk Hess
m
ade com
b
inati
o
n of tpi and
pme work again i
n
parallel
commit
|
commitdiff
|
tree
2010-10-08
Berk H
e
ss
fixed c
o
m
binati
o
n of
tpic
w
ith pm
e
,
p
m
e
mesh energy
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Berk
Hess
ma
d
e g
r
o
mpp md
p
inpu
t
file non-optional, fixe
s
bugzill
a
57
7
commit
|
commitdiff
|
tree
2010-10-05
Berk
H
es
s
added fa
i
l-
s
afe c
h
eck
for
O
penMM with
d
ouble precision
commit
|
commitdiff
|
tree
2010-10-05
Ber
k
Hess
renam
e
d mdp sett
i
ng Ace-approx to
A
c
e-approximation
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
fixe
d
c
omp
l
etely incorrect pressure sc
a
l
i
ng
with n
s
tlis
t
.
.
.
commit
|
commitdiff
|
tree
2010-09-30
B
erk
Hess
change
d
the grom
p
p charge group radii to a
l
ways check
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Berk Hess
fixed case of
o
p
l
s atom type
s
in s
h
are/top/ions
.
it
p
.
.
.
commit
|
commitdiff
|
tree
2010-09-22
Berk Hess
added a warning/not
e
for bond
os
c
illati
o
nal perio
d
s
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Berk Hess
a
d
d
e
d check for ta
u
_t<=
0
w
it
h
int
e
grat
o
r sd
commit
|
commitdiff
|
tree
2010-09-21
Berk Hess
fixed incorr
e
ct
gmxch
e
ck comparison of ir->sep
a
rate_dhdl_file
commit
|
commitdiff
|
tree
2010-09-21
Berk H
e
ss
i
mproved
the initial gu
e
ss and
fitti
n
g
w
eights for
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Be
r
k Hess
removed g_analyze confusing fittin
g
messages about
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Berk
H
e
s
s
fi
x
ed too small fixed array in grompp
t
op r
e
ading
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
B
e
r
k Hess
Re
v
e
rt
"
added GB non-
p
o
l
ar solvatio
n
energy ter
m
t
o
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Ber
k
Hess
added GB non-polar solvation energ
y
term to
t
he log
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Ber
k
Hes
s
f
ixed free-energy giving a fatal-
e
rror w
h
en GB12, GB
1
3
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Ber
k
Hess
added hint to g_tr
a
j warning
commit
|
commitdiff
|
tree
2010-09-16
Berk
H
ess
fixed the maximum
p
rint f
o
r g_tra
j
-cv and -cf
commit
|
commitdiff
|
tree
2010-09-16
Berk He
s
s
f
i
xed some mino
r
issu
e
s with g_t
r
aj
-
cv and -cf
commit
|
commitdiff
|
tree
2010-09-16
Ber
k
Hes
s
tau_t=-
1
now works i
n
grompp and
with SD
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
fi
x
ed g_traj segv when ran without pbc
commit
|
commitdiff
|
tree
2010-09-15
Be
r
k
H
ess
fixed charg
e
group
r
a
dius LJ che
c
k,
wh
i
ch
coul
d
produce
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added missin
g
F
_
P
IDIHS ca
s
e
to topsor
t
free energy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk
Hess
a
d
d
ed GM
X
_MAX_THRE
A
DS env
.
var
.
to set
the max
i
mum number
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk He
s
s
fixed
m
emor
y
allocation a
n
d ac
c
ess issues
w
he
n
reading
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
B
erk
H
ess
grompp
opt
i
on
-
pp
n
o
w always writ
e
s to cwd
commit
|
commitdiff
|
tree
2010-09-14
Berk H
e
s
s
g_density now norma
l
ize
s
every frame sep
a
ratel
y
commit
|
commitdiff
|
tree
2010-09-14
Berk H
e
ss
g_density now normal
i
z
es with the a
v
erage volu
m
e
i
ns
t
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
B
erk Hess
fixed incorrect r
e
ferenc
e
posit
i
on of position restr
a
ints
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
fix
e
d gro
m
pp -t f
r
ame choi
c
e
for trajectories with
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
s
t
ate
switches be
t
ween t
h
e cpt and tp
r
fi
l
e in mdrun
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk H
e
ss
added check an
d
w
arning for no velocities in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Be
r
k Hess
tur
n
e
d on che
c
kpointing
with nstlist=0
commit
|
commitdiff
|
tree
2010-09-10
Berk
H
es
s
rem
o
ved the lower bound
c
heck on test pa
r
ticle inse
r
tion
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
removed t
i
p5p fr
o
m charmm27
.
f
f
/watermodels
.
dat,
si
n
ce
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
made
s
ure
the ener
g
y
hist
o
r
y f
r
om a check
p
o
i
nt f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Berk Hess
added SSE overflow ch
e
ck for TPI
commit
|
commitdiff
|
tree
2010-09-09
Berk Hess
t
h
e force tables are now co
n
ti
n
u
ed linearly f
r
om nearl
y
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk Hess
improved the automatic choice of t
h
e number of
PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk Hess
a
d
ded MCH3
S
a
t
om t
y
pe for Cha
r
mm
for virtua
l
sites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk
H
ess
changed the o
r
der
of
the
outer lo
o
ps in the fft
5
d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
r
emove
d
empty
edr and xtc
f
i
les with
nm
commit
|
commitdiff
|
tree
2010-09-07
Berk H
e
ss
removed
(
n
a
n) average pr
i
nting with normal modes
commit
|
commitdiff
|
tree
2010-09-07
Ber
k
Hess
fixed crash with
p
arallel nm with cut-of
f
'
s
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoid
e
d creati
o
n of neigh
b
orlists without j-particles
commit
|
commitdiff
|
tree
2010-08-26
B
erk
H
ess
fixed bug that ca
u
sed c
o
rrupted checkpo
i
nt
f
iles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
pdb2gmx now only allow
s
a m
i
smatch of a sign (iso a
n
y
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
fi
x
ed pd
b
2
g
mx usi
n
g start n
a
me iso end name for
C
-term
i
nus
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixed bug
i
n
searc
h
_rtp
i
ntroduc
e
d in previous commit
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
up
d
ated gmx
_
membed
.
c for
a VV update
commit
|
commitdiff
|
tree
2010-08-24
Be
r
k Hes
s
f
ixed pdb2gmx behavi
o
r
fo
r
nea
r
ly
matchi
n
g residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
B
e
rk Hess
re
m
oved t
h
e pdb
2
gmx
-
cwd option and
upd
a
ted the pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
H
e
ss
pd
b
2
gmx now prints
t
h
e
force field
d
ir before the
selecti
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
fixed mpi hang/crash with se
p
a
r
a
te
pme nod
e
s and
d
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
ad
d
e
d
fun
c
tion do_cpte_n_reals to c
h
eckp
o
int
.
c
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk Hess
fixed automated
DD/PME gri
d
decomposition choice whic
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
Hess
disabled
optimized IBM BlueGene converts2int
s
macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
B
erk He
s
s
increased tp
x
_g
e
ne
r
at
i
on which
should have been done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
B
er
k
Hess
eneconv
n
ow copi
e
s
the
n
ew delta_t entry
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k H
e
ss
a
d
ded dt to energy file f
r
am
e
s
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk H
e
ss
added free
an
d
s
o
m
e
c
o
m
ment to deprecated clos
e
_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed segv's
i
n g_anaeig
commit
|
commitdiff
|
tree
2010-08-18
B
erk Hess
reduced the warnin
g
limit
f
o
r Ber
e
ndsen
T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Ber
k
Hess
removed the
b
NEMD
b
oolean
from the mai
n
MD
l
oop and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added some comment to group grompp assi
g
nment
o
ptions
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
adde
d
group compar
i
son to gmxcheck and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
fixe
d
possible p
a
the string buffer o
v
erf
l
ow
in get_libdir
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
adde
d
funct
i
on rescal
e
_veloci
t
ies
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
gmx_rmpbc now guesses ePBC again
f
o
r
eac
h
frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
g
m
x_rmpbc gets
na
t
oms
pa
s
s
ed ag
a
i
n, without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
p
ut omp
pragma's i
n
fft5d
.
c
betw
e
en ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
added openmp pragma's for the f
f
t
5d
tran
s
pose routines
commit
|
commitdiff
|
tree
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