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fixed segv in grompp due to gmxcpp not checking for #include statements without delim...
2010-11-24
Berk Hess
fixed
s
egv
i
n
gro
m
pp due to g
m
x
cpp
not checking for
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
Berk Hess
pdb
2
gmx now puts atoms wit
h
cgnr=-1 in separat
e
charge
.
.
.
commit
|
commitdiff
|
tree
2010-11-04
B
erk Hess
Fi
x
e
d md
.
log
being open
e
d twice
when appending, whi
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Be
r
k Hess
f
i
xed incorrect print in
fatal err
o
r on char
g
e
g
roup
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Ber
k
Hess
proper defined of
M
AX_CHARGEGROUP_SIZE=32 i
n
a singl
e
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
Berk Hess
added HEM to HEME renaming for Gromos a
n
d Ch
a
rmm ff's
commit
|
commitdiff
|
tree
2010-10-28
Berk
H
ess
fixed pd
b
2gmx chain me
r
ging bug (bugzi
l
l
a
5
44)
commit
|
commitdiff
|
tree
2010-10-26
B
e
rk Hess
fixed cycle print type cas
t
iss
u
e on certain platforms
.
.
.
commit
|
commitdiff
|
tree
2010-10-21
Berk Hes
s
clarified make_ndx error message
commit
|
commitdiff
|
tree
2010-10-19
Berk Hess
changed en
x
io warning i
n
t
o fat
a
l
e
rrors by default
.
.
.
commit
|
commitdiff
|
tree
2010-10-18
Berk Hess
fi
x
ed atom type
n
a
m
e
case fo
r
m
e
thanol
.
itp in gromos43a1
.
ff
commit
|
commitdiff
|
tree
2010-10-18
B
erk Hes
s
fixe
d
p
o
ssible
overflow of unused variable in
l
incs
commit
|
commitdiff
|
tree
2010-10-18
Berk He
s
s
added
checks f
o
r
r
are events that would make variables
.
.
.
commit
|
commitdiff
|
tree
2010-10-15
B
e
r
k Hess
more fixes for
TPI with PME, now
really fixed bugzil
l
a 590
commit
|
commitdiff
|
tree
2010-10-13
Berk Hess
fi
x
ed g_ve
l
acc -m not automatical
l
y usin
g
-s
commit
|
commitdiff
|
tree
2010-10-12
Be
r
k Hess
a
dded n
o
te to g_den
s
ity for
u
sin
g
g
_energy for nor
m
al
.
.
.
commit
|
commitdiff
|
tree
2010-10-12
Ber
k
Hess
fixed incorrec
t
dispersi
o
n correction for TPI
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
Berk Hess
fi
x
ed typo in checkpoint warning
commit
|
commitdiff
|
tree
2010-10-08
Berk Hess
made
combina
t
ion of
tpi a
n
d
p
me
work aga
i
n in
p
arallel
commit
|
commitdiff
|
tree
2010-10-08
Be
r
k Hess
fixed c
o
mbination of tpic
w
i
t
h
pme, pme mesh
e
n
ergy
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Be
r
k
Hess
m
a
de
g
r
ompp mdp
i
nput file no
n
-optional
,
fixes bugzilla 577
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
adde
d
fail-safe che
c
k for OpenM
M
with double precision
commit
|
commitdiff
|
tree
2010-10-05
Berk He
s
s
renamed
m
dp
se
t
ting Ace-ap
p
rox to Ace
-
approximation
commit
|
commitdiff
|
tree
2010-10-05
Berk H
e
s
s
fi
x
ed completely
i
ncorr
e
c
t
pressure scaling with nstlist
.
.
.
commit
|
commitdiff
|
tree
2010-09-30
Berk H
e
ss
chang
e
d the grompp charge grou
p
radii to always check
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Berk Hess
fixed case of
o
pls atom
types in share
/
top/ion
s
.
itp
.
.
.
commit
|
commitdiff
|
tree
2010-09-22
Berk Hess
a
d
d
ed a
w
arning/
n
ote for bond oscillational
p
e
r
i
o
ds
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Ber
k
Hess
added
c
heck for
tau_t
<
=
0
wit
h
i
n
tegrator sd
commit
|
commitdiff
|
tree
2010-09-21
B
e
rk
Hess
fixed incorrec
t
gmxc
h
eck
comparison of ir->sepa
r
ate_dhd
l
_file
commit
|
commitdiff
|
tree
2010-09-21
B
erk Hess
improved the initial guess and
f
itting weigh
t
s
for
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
B
e
rk Hess
removed g_analyze confusing fitting
m
e
s
s
ages
a
bout
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Berk
H
ess
fi
x
ed too sma
l
l
f
ixed
a
r
ra
y
in
grompp top reading
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
Rev
e
rt
"added GB non-polar solva
t
ion en
e
r
gy ter
m
to
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk
Hess
added G
B
non-polar solva
t
ion en
e
rgy term to the
l
og
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
B
e
r
k
H
ess
fixed free-energy giving a fatal-error when GB12, GB1
3
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
B
e
r
k
Hess
added hint to
g_t
r
aj
w
a
r
ning
commit
|
commitdiff
|
tree
2010-09-16
Berk He
s
s
fixed the m
a
x
i
mum print for g_traj -cv
and -cf
commit
|
commitdiff
|
tree
2010-09-16
Berk
Hess
fixe
d
some
m
inor is
s
ues wi
t
h g_traj -cv and -cf
commit
|
commitdiff
|
tree
2010-09-16
Berk
H
ess
t
au_t=-1 now wor
k
s in grompp a
n
d with SD
commit
|
commitdiff
|
tree
2010-09-15
B
erk
H
ess
f
i
x
ed g_
t
raj segv w
h
en ran
w
ithout pbc
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
f
ixed charge group
ra
d
iu
s
LJ
c
h
e
ck, which could produc
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
a
d
d
e
d missing F_PIDIHS case
to topsort free e
n
ergy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added GMX_MAX_THREADS
e
nv
.
var
.
t
o set
t
he maximum
n
umber
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Ber
k
Hess
fixe
d
memory allocat
i
on and acces
s
issue
s
when reading
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
grompp option -pp now always
w
r
ites to cwd
commit
|
commitdiff
|
tree
2010-09-14
B
erk
Hess
g_d
e
nsity now normalizes eve
r
y f
r
ame separat
e
ly
commit
|
commitdiff
|
tree
2010-09-14
B
erk
Hess
g_d
e
nsity now normalizes with the average v
o
lume inst
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
f
i
xed incorrect reference po
s
iti
o
n of posi
t
ion restraints
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk
H
ess
fixed grompp -t
f
ra
m
e choice f
o
r trajector
i
es with
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
s
t
at
e
s
witches betwee
n
the cpt and tpr file in mdrun
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
B
e
rk
H
e
ss
ad
d
e
d
c
h
eck and warning
f
or
n
o ve
l
ociti
e
s in g
r
o
m
p
p
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
turned on checkp
o
i
nting
w
it
h
nstlist=0
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
remove
d
t
h
e lower bo
u
n
d
c
heck
on
test particle i
n
sertion
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Ber
k
Hess
re
m
ov
e
d
tip5p f
r
om charm
m
27
.
ff/wa
t
ermodels
.
da
t
, since
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Be
r
k Hess
mad
e
sur
e
the
ener
g
y history fr
o
m a che
c
k
point file
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Berk Hess
add
e
d
SSE overflow c
h
eck for TPI
commit
|
commitdiff
|
tree
2010-09-09
B
e
rk Hes
s
the force tab
l
e
s
are now continued l
i
nearly
from nearly
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk
H
e
s
s
improved the
a
utoma
t
ic choice of the
n
umber of PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
B
erk Hess
added MCH3S atom
t
ype for Charmm for v
i
rtual s
i
tes
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
changed the order
of the outer loops
i
n
t
he fft5d tran
s
po
s
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk H
e
s
s
r
emov
e
d empty edr and xtc fi
l
es wi
t
h nm
commit
|
commitdiff
|
tree
2010-09-07
B
erk Hess
re
m
ov
e
d (nan) a
v
erag
e
printing with no
r
mal
modes
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
fixed
c
rash with paral
l
el nm with
cut-off's
commit
|
commitdiff
|
tree
2010-08-31
B
e
rk Hes
s
a
voided creation of ne
i
ghborlist
s
w
i
thout
j
-
p
articles
commit
|
commitdiff
|
tree
2010-08-26
B
e
rk
Hes
s
f
i
xed bug that caused corrupted checkpoint file
s
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
pdb2gmx now only al
l
ow
s
a mi
s
match of a
s
ign
(
i
so any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
f
i
xed
pdb2gmx
using start
nam
e
i
so e
n
d name fo
r
C-ter
m
inus
commit
|
commitdiff
|
tree
2010-08-24
B
e
r
k Hess
fixed bug in search_rtp introduced in previous commit
commit
|
commitdiff
|
tree
2010-08-24
Be
r
k
H
ess
upd
a
te
d
gmx_membed
.
c for a VV update
commit
|
commitdiff
|
tree
2010-08-24
B
er
k
Hess
fixed
pdb2gmx
beh
a
vio
r
f
or nearly matching
r
esidue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
rem
o
ved the pdb2gmx -cwd optio
n
a
n
d u
p
da
t
ed the pdb2gm
x
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
pd
b
2gmx now prints the forc
e
fiel
d
dir b
e
fore
the selec
t
ion
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
fixed m
p
i ha
n
g/crash with separat
e
pme nodes and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added
f
unction do_cpte_n_reals to
c
heckp
o
i
n
t
.
c
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed autom
a
ted
DD/PME grid deco
m
posi
t
ion choice whi
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk Hess
d
i
sabled optimized IBM BlueGene converts2i
n
ts ma
c
ro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
inc
r
eased tpx_generation which should
h
ave been don
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
eneconv now copies
t
he
n
ew delta_
t
entry
commit
|
commitdiff
|
tree
2010-08-20
B
erk Hess
added dt to
energy file
fram
e
s
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
added f
r
ee and so
m
e comment to depreca
t
ed clos
e
_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixe
d
s
egv's in g_anaeig
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduced
the warning l
i
mit fo
r
Ber
e
nd
s
en
T
-c
o
u
pling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
re
m
ove
d
t
he bN
E
MD boolean
from
t
h
e
m
ai
n
M
D
loop
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
add
e
d some commen
t
to group grompp assignment opti
o
ns
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added group comparison to gmxchec
k
and
p
rint groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
fi
x
ed possibl
e
pathe string buffer overflow
i
n
g
et_
l
ibdir
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
added f
u
nction rescale_velocities
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
gmx_rm
p
bc now guesses ePBC again for each frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc gets natoms passed again,
without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
He
s
s
put omp
p
r
a
g
ma
'
s in fft
5
d
.
c b
e
t
w
e
en ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k
He
s
s
adde
d
openmp prag
m
a's for
t
h
e
fft5d tra
n
spose
routin
e
s
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed mdrun
w
ri
t
es tpidist
.
xvg
o
n all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fix
e
d se
g
v
in mdr
u
n wi
t
h replica exchange
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fi
x
ed
f
atal err
o
r in md
r
un file a
p
pen
d
ing with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk H
e
ss
gmxcheck
n
ow prints rmsd's as %g i
s
o %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
moved f
u
ll
precision
real
f
ormat de
f
inition
t
o simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
r
e
verted the last, non-cosmetic change
to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
minor co
s
metic changes in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Be
r
k Hes
s
made
the
pd
b
2
gmx occup
a
ncy warning more obvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hes
s
fix
e
d incorrect pdb2
g
mx output with
m
ultiple (altloc
.
.
.
commit
|
commitdiff
|
tree
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