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fixed zero viscosity energy/log file output with cos_acceleration
2011-01-10
Be
r
k He
s
s
fixed
zero
v
iscosi
t
y e
n
ergy/log
f
ile outp
u
t
with cos_acce
l
e
r
.
.
.
commit
|
commitdiff
|
tree
2011-01-04
Berk H
e
s
s
f
i
xed g
r
ompp looki
n
g
for include fi
l
es in double relative
.
.
.
commit
|
commitdiff
|
tree
2010-12-22
Be
r
k He
s
s
removed
incorrec
t
citation pri
n
t of Engin2010 for pull
.
.
.
commit
|
commitdiff
|
tree
2010-12-21
Berk H
e
ss
pm
e
.
c work-around for
MPI fat
a
l err
o
r in pme w
i
th partt
i
cle
.
.
.
commit
|
commitdiff
|
tree
2010-12-16
Ber
k
Hess
fixed incorrect LJ table in
mdr
u
n with
reppow!=1
2
commit
|
commitdiff
|
tree
2010-12-16
B
erk Hes
s
removed e
d
itconf w
a
r
n
i
n
g on box distance
w
ith -b
t
commit
|
commitdiff
|
tree
2010-12-13
Berk Hess
fixed tpb
c
onv
time option
s
leading t
o
negative nsteps
.
.
.
commit
|
commitdiff
|
tree
2010-11-24
Berk Hess
fixed se
g
v in
gr
o
mpp due
t
o gmxcpp
not che
c
king
for
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
B
erk H
e
ss
added -resnr option to editconf
commit
|
commitdiff
|
tree
2010-11-09
B
e
rk
He
s
s
fixed compiler w
a
rning
i
n
pdb2gmx
.
c
commit
|
commitdiff
|
tree
2010-11-05
Berk He
s
s
pdb2gmx
n
ow puts
a
toms
w
ith c
g
n
r=
-
1 in separate charge
.
.
.
commit
|
commitdiff
|
tree
2010-11-04
Berk H
e
s
s
Fixed md
.
log being opened twice when ap
p
ending, which
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
B
erk He
s
s
fixed inco
r
rect print in f
a
tal error o
n
cha
r
ge group
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
B
erk Hes
s
p
r
oper defined of MAX
_
CHARGEGROUP_SIZE
=
3
2 in a single
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
Berk Hess
added H
E
M to HEME renamin
g
for Grom
o
s and
Charm
m
ff's
commit
|
commitdiff
|
tree
2010-10-28
B
e
rk Hess
fixed pdb2
g
mx chain
m
erging
bug (bugzill
a
54
4
)
commit
|
commitdiff
|
tree
2010-10-26
Berk He
s
s
fi
x
ed
c
ycle print
t
ype cast iss
u
e on certai
n
platforms
.
.
.
commit
|
commitdiff
|
tree
2010-10-21
Berk Hess
clarified make_
n
dx err
o
r message
commit
|
commitdiff
|
tree
2010-10-19
Berk Hess
changed enxio warn
i
ng into
fat
a
l
erro
r
s by default
.
.
.
commit
|
commitdiff
|
tree
2010-10-18
Ber
k
Hess
fixed atom type
n
a
me
ca
s
e for
m
etha
n
ol
.
itp in gro
m
o
s
43a1
.
ff
commit
|
commitdiff
|
tree
2010-10-18
Berk
Hess
fixed possi
b
le ove
r
flow of unused variable in
l
inc
s
commit
|
commitdiff
|
tree
2010-10-18
Be
r
k Hess
a
dd
e
d checks fo
r
rare
events that would make variables
.
.
.
commit
|
commitdiff
|
tree
2010-10-15
Berk Hess
more fix
e
s for TPI
with PME, now
r
eally fix
e
d bu
g
z
ill
a
590
commit
|
commitdiff
|
tree
2010-10-13
Berk
H
ess
fixed g_velacc -m n
o
t automatically us
i
ng -s
commit
|
commitdiff
|
tree
2010-10-12
Berk Hess
a
dded note to g_d
e
nsity for usi
n
g g_en
e
r
gy
fo
r
normal
.
.
.
commit
|
commitdiff
|
tree
2010-10-12
Berk He
s
s
fix
e
d incor
r
ect di
s
persion corr
e
c
t
ion for TPI with
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
Berk Hess
fixe
d
typo in checkpoin
t
warnin
g
commit
|
commitdiff
|
tree
2010-10-08
Berk
Hess
made c
o
mbinati
o
n of tpi
and pme
work again in par
a
llel
commit
|
commitdiff
|
tree
2010-10-08
Ber
k
He
s
s
fix
e
d combinati
o
n
of tpic with pme
,
pme mesh energy
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
Ber
k
Hess
made grompp mdp
i
nput file non-optional, fixes b
u
gzilla 577
commit
|
commitdiff
|
tree
2010-10-05
B
e
rk Hess
added fail
-
safe c
h
eck for Op
e
nMM
wit
h
d
o
u
ble
p
rec
i
sion
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
renamed mdp s
e
tting Ace-approx to Ac
e
-app
r
oximation
commit
|
commitdiff
|
tree
2010-10-05
Berk Hes
s
fixed completely
i
ncorrec
t
p
r
essure scal
i
ng wit
h
nstli
s
t
.
.
.
commit
|
commitdiff
|
tree
2010-09-30
Berk
H
es
s
changed the g
r
ompp char
g
e gro
u
p radi
i
to always check
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Berk He
s
s
fixed case of opls a
t
om ty
p
e
s
in sh
a
re/top/io
n
s
.
itp
.
.
.
commit
|
commitdiff
|
tree
2010-09-22
Berk Hess
added a
w
ar
n
ing/
n
o
te
f
o
r
b
ond oscillationa
l
p
eriods
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Berk Hess
adde
d
c
heck for t
a
u_t<=0 with integrator sd
commit
|
commitdiff
|
tree
2010-09-21
B
erk Hess
fixe
d
incorrect gmxcheck comparison of ir->s
e
p
a
rat
e
_dhdl_file
commit
|
commitdiff
|
tree
2010-09-21
Berk Hess
improved the initial g
u
ess and fitting weigh
t
s for
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
B
erk Hess
removed g_an
a
lyze confusin
g
f
i
tting m
e
ssages abo
u
t
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Berk
H
e
s
s
f
i
xed to
o
sm
a
l
l
f
i
xed array in grompp
t
op
r
ead
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk
Hess
Revert "adde
d
GB non-polar solvation energy te
r
m to
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
adde
d
GB n
o
n-p
o
lar solvation energy
t
e
r
m
t
o
th
e
log
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
fixed free-ener
g
y giv
i
n
g a fatal-error when
G
B12
,
GB13
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
B
e
r
k Hess
added hint t
o
g
_
traj
w
arning
commit
|
commitdiff
|
tree
2010-09-16
Berk Hess
fixed the maximum print for g_traj -cv and -cf
commit
|
commitdiff
|
tree
2010-09-16
Ber
k
He
s
s
f
i
xed some minor issues with g_traj -cv
a
nd -
c
f
commit
|
commitdiff
|
tree
2010-09-16
B
er
k
H
e
ss
tau_t=-1 now
w
o
rks in grompp and with SD
commit
|
commitdiff
|
tree
2010-09-15
Berk
H
ess
fixed g_traj
segv
w
hen ran with
o
ut pbc
commit
|
commitdiff
|
tree
2010-09-15
B
e
rk Hess
fi
x
e
d
c
harge grou
p
radiu
s
LJ check
,
w
h
i
c
h
cou
l
d produce
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added missing F_P
I
DIHS case to topsort f
r
e
e energy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added G
M
X_MAX_THREADS env
.
va
r
.
t
o
set
the maxi
m
um numb
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
B
e
r
k
He
s
s
f
ixed memory allocation
a
nd access issues when
read
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk
Hess
grompp opti
o
n -
p
p now a
l
ways writes to cwd
commit
|
commitdiff
|
tree
2010-09-14
Berk H
e
ss
g
_
density now n
o
rmalizes
e
v
ery frame
s
eparately
commit
|
commitdiff
|
tree
2010-09-14
Berk He
s
s
g_density now norma
l
i
zes with the
a
verage volume instead
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
B
erk
H
ess
fixe
d
incorr
e
ct
r
efere
n
c
e
position o
f
positio
n
restraints
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
B
e
rk Hess
fixed
gr
o
mpp -t frame cho
i
ce
for
t
raje
c
t
o
ries with
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
s
t
ate switches b
e
tween
the cpt and
t
pr f
i
le in
m
drun
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk H
e
ss
added
check and warning f
o
r no velociti
e
s in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
B
erk
Hess
turn
e
d on chec
k
pointing with nstlist=0
commit
|
commitdiff
|
tree
2010-09-10
Be
r
k Hess
r
em
o
ved t
h
e low
e
r bo
u
n
d
check on
t
est parti
c
le insertio
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk He
s
s
removed tip5
p
from
ch
a
rmm2
7
.
ff/watermodel
s
.
d
at, sin
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
B
er
k
Hess
ma
d
e su
r
e th
e
e
n
ergy history from a che
c
kpoint fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Berk
Hess
added
SSE overflow
c
heck for
T
PI
commit
|
commitdiff
|
tree
2010-09-09
Berk Hess
the fo
r
ce tables are
n
ow continu
e
d linearly
f
r
o
m ne
a
rly
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Be
r
k Hess
improved the automatic cho
i
ce
of the
n
u
mber of PM
E
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk
H
ess
added MCH3S atom type for C
h
a
r
mm for
v
irtual sites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk
H
e
s
s
changed the order of
t
he outer loo
p
s i
n
the fft5d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk H
e
ss
removed
e
m
p
t
y
edr
a
nd xtc files with nm
commit
|
commitdiff
|
tree
2010-09-07
Be
r
k Hess
r
emove
d
(nan) average
printing with normal m
o
de
s
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
fixed c
r
ash with par
a
l
l
el
n
m with cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hes
s
avoide
d
creation o
f
neighborlists wi
t
hout
j-particles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
fixed bug that
c
aused corrupted checkpoint files
commit
|
commitdiff
|
tree
2010-08-26
Be
r
k He
s
s
pdb2gmx now
o
n
l
y
a
l
l
ows
a
mismatch o
f
a sign (iso a
n
y
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
f
i
x
ed pdb2gmx using start
n
ame is
o
end name f
o
r C-
t
ermi
n
us
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
s
s
fixed bug i
n
search_rtp intr
o
duced in
p
revi
o
us commit
commit
|
commitdiff
|
tree
2010-08-24
Berk
H
ess
u
p
dated
g
mx_mem
b
ed
.
c
for a VV upd
a
te
commit
|
commitdiff
|
tree
2010-08-24
Berk
H
e
s
s
fixed
pdb2
g
mx be
h
avi
o
r for nearly matching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
Hess
r
e
m
oved the pdb2gmx
-
c
w
d
o
pt
i
o
n
and updated
t
he pd
b
2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k H
e
ss
pd
b
2
g
mx now p
r
int
s
the
f
orce field
d
i
r before t
h
e
selecti
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
fixed mpi hang/
c
r
a
sh with sep
a
ra
t
e pme
n
odes and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k
Hess
added function d
o
_
cpte_n_r
e
als
to checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed a
u
tomate
d
DD/PME grid d
e
c
o
mposi
t
ion choice which
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
disa
b
led
o
ptimized IBM Bl
u
eGene c
o
n
v
erts2ints macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
B
e
r
k Hess
incr
e
ased tpx_generation which sho
u
ld have
b
e
e
n
d
o
ne
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k Hess
eneco
n
v now copi
e
s the new delta_t entry
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk Hes
s
a
d
d
e
d
d
t to energy file
f
r
a
mes
commit
|
commitdiff
|
tree
2010-08-20
Berk H
e
ss
adde
d
free and s
o
me commen
t
to deprecated close_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed segv
'
s in g_anaeig
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduced the wa
r
ning li
m
it
for Berendsen T-coup
l
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
remov
e
d
t
h
e
bNEMD boolean
f
r
om the main M
D
l
oo
p
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added some c
o
mment to grou
p
grompp assignment options
commit
|
commitdiff
|
tree
2010-08-18
Berk Hes
s
added gr
o
u
p c
o
mpa
r
ison
t
o
g
m
xchec
k
a
n
d prin
t
gro
u
ps
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
fixed possible
p
athe stri
n
g buffer
overflow in get_l
i
bdir
commit
|
commitdiff
|
tree
2010-08-17
B
e
rk H
e
ss
added fu
n
ct
i
on rescale_velocities
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc now gues
s
es
ePBC agai
n
for each frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gm
x
_rmpbc gets natom
s
passed
again
,
without n
a
toms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk
Hes
s
put omp pra
g
ma's in fft5d
.
c between
i
f
def's
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
added
o
p
enmp
p
ra
g
ma's for the fft5d
t
ranspose rou
t
in
e
s
commit
|
commitdiff
|
tree
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