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fixed trjconv not writing velocities with cpt input
2010-09-21
Berk Hess
fixed incorrect gmxcheck comparison o
f
ir->s
e
p
arate_dhdl_fi
l
e
commit
|
commitdiff
|
tree
2010-09-21
Berk Hess
i
m
proved the
i
n
i
tial gues
s
a
n
d
fit
t
ing
w
ei
g
ht
s
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Berk
Hess
removed g_anal
y
ze confusing fitting mes
s
a
ges abou
t
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Berk
H
ess
fixed too small fixed array in grompp
top re
a
d
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
Revert "added
GB
n
on-polar sol
v
ati
o
n energy term
t
o
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
added GB non-
p
olar solvation ene
r
gy t
e
rm to the log
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
fixed free
-
en
e
rgy
g
iving a fatal-error wh
e
n
GB12, GB13
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Be
r
k
Hess
added
hin
t
to g_traj w
a
rning
commit
|
commitdiff
|
tree
2010-09-16
B
erk Hess
fixed the
m
aximu
m
print for
g_tr
a
j -c
v
an
d
-
cf
commit
|
commitdiff
|
tree
2010-09-16
Ber
k
H
e
ss
fixe
d
some minor issues with g_traj
-cv an
d
-cf
commit
|
commitdiff
|
tree
2010-09-16
Be
r
k Hess
tau_t=-1 now works
i
n g
r
ompp and with S
D
commit
|
commitdiff
|
tree
2010-09-15
B
erk Hess
f
i
x
e
d g_traj segv
w
hen ran without pb
c
commit
|
commitdiff
|
tree
2010-09-15
Be
r
k
Hes
s
fixed ch
a
rge g
r
ou
p
radius LJ check, wh
i
ch
c
ould produc
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hes
s
added
missing F_
P
IDIHS
case to to
p
so
r
t
free e
n
ergy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk H
e
ss
added GMX_MAX_THR
E
A
D
S
env
.
var
.
to set the maxim
u
m n
u
mber
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
fixed memory a
l
location and acces
s
issu
e
s
w
h
en r
e
ading
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
grom
p
p
o
ption
-
pp now always writes to cwd
commit
|
commitdiff
|
tree
2010-09-14
Be
r
k H
e
ss
g
_
densit
y
now nor
m
alizes
ever
y
fram
e
s
e
p
arately
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
g_densi
t
y now normaliz
e
s
w
ith the ave
r
ag
e
vol
u
me in
s
tead
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Be
r
k Hess
fixed incorrect reference
p
osi
t
ion of position re
s
traints
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk
Hess
fixed grompp -t
frame choice
for traj
e
ctories w
i
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
state switches between the cpt and tpr file in mdr
u
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hes
s
added check
a
nd warning for no velocities in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Ber
k
Hess
t
u
rn
e
d on check
p
oi
n
ting with
nstlist=0
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
r
e
moved the lower
b
ound ch
e
ck on t
e
st particle i
n
sertion
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Be
r
k Hess
r
e
m
oved t
i
p
5
p
from charmm
2
7
.
ff/watermodels
.
dat,
since
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
made sure the energy history
from a checkpoint
f
ile
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Be
r
k Hess
added SSE o
v
erflow check for TPI
commit
|
commitdiff
|
tree
2010-09-09
Berk H
e
ss
t
h
e force table
s
ar
e
no
w
c
ontinued linear
l
y from
n
early
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk
H
e
ss
im
p
roved
the automatic cho
i
ce of t
h
e number of PM
E
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Ber
k
H
ess
added MCH3S atom type for
C
harmm for virt
u
al
s
ites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
changed
the
order of the
o
u
t
er
lo
o
ps in
t
he
f
ft5d tra
n
sp
o
se
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
re
m
oved empty edr and
xt
c
f
il
e
s
with nm
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
re
m
oved (n
a
n) average
p
rinting with normal modes
commit
|
commitdiff
|
tree
2010-09-07
Berk
He
s
s
f
ixed cra
s
h with parallel nm with cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided creatio
n
of neighb
o
rlis
t
s witho
u
t j-particl
e
s
commit
|
commitdiff
|
tree
2010-08-26
Berk He
s
s
fixed bug that
cau
s
ed c
o
rrupted check
p
o
i
nt fi
l
es
commit
|
commitdiff
|
tree
2010-08-26
Be
r
k He
s
s
pdb
2
gmx now only allows a
m
i
s
match o
f
a sign (iso any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
f
ixed pdb2gmx using star
t
name iso end name for C-te
r
minu
s
commit
|
commitdiff
|
tree
2010-08-24
Be
r
k Hess
fix
e
d bug in sea
r
c
h
_rtp introd
u
c
e
d
i
n
pr
e
v
i
o
u
s
c
ommit
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
updated
g
mx_membed
.
c for a VV
u
p
d
a
t
e
commit
|
commitdiff
|
tree
2010-08-24
Ber
k
H
ess
fixed pdb2
g
mx behavio
r
for nearly matching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k He
s
s
remo
v
e
d
the
p
db2gmx -
c
wd option a
n
d updated the pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k
H
ess
p
db2gmx now p
r
ints t
h
e for
c
e
field dir before the selection
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
fixed m
p
i
hang
/
crash with separate
p
m
e nodes and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added function do_cpte_n_r
e
als to checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
Hess
fixe
d
au
t
omated DD/PME grid decomp
o
s
ition choice
w
h
i
ch
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
disabled
op
t
i
mized IBM BlueGene con
v
erts2
i
nts mac
r
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
increased
t
p
x_
g
eneratio
n
whi
c
h
should have been done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
eneconv now copies
t
he
n
ew delta_
t
entry
commit
|
commitdiff
|
tree
2010-08-20
Berk He
s
s
added d
t
to
en
e
rgy
file frame
s
commit
|
commitdiff
|
tree
2010-08-20
Berk H
e
ss
a
dded free
and some comment
to dep
r
e
cated c
l
ose_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed segv's in g_anaeig
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduced
t
h
e warning limi
t
f
or
Berendsen T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
removed the
b
NEMD b
o
o
lean from
t
he main MD loop and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added some comment
t
o
g
roup
grompp assignment options
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
ad
d
ed group comparison
to gmxc
h
eck and pr
i
nt groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
fixed possible pathe s
t
ring buffer overflo
w
in get_libdir
commit
|
commitdiff
|
tree
2010-08-17
Ber
k
Hess
added functi
o
n resc
a
l
e_velocities
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_
r
mpbc now
g
uesses
ePBC again
for each fr
a
me
commit
|
commitdiff
|
tree
2010-08-16
B
erk
Hess
gmx_rmpbc gets natoms passed again, without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
put
omp prag
m
a's in
fft5d
.
c between ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
a
dded open
m
p
p
r
a
gma's for the fft5d transpose
r
o
u
t
ines
commit
|
commitdiff
|
tree
2010-08-16
Berk
H
ess
fi
x
e
d
mdrun writes tpidi
s
t
.
xvg
o
n all nodes
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
fixe
d
segv in mdrun with repli
c
a exchange
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
f
i
x
ed fata
l
er
r
or in mdrun
file appendin
g
with -mult
i
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Ber
k
Hes
s
gmxcheck
now
p
rints rmsd's as %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
moved full
precision re
a
l format definition to s
i
m
ple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
revert
e
d the last, non-cos
m
etic c
h
ange to
p
m
e
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
minor
cosme
t
ic changes in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk H
e
ss
made t
h
e
pdb2gmx occ
u
pancy warning more
obvious
commit
|
commitdiff
|
tree
2010-08-12
B
e
rk Hess
fixe
d
in
c
orrect pdb2gmx output
wit
h
multipl
e
(altl
o
c
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk H
e
ss
rem
o
ved -merge fr
o
m the
p
db2g
m
x manual and clar
i
fied
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Be
r
k H
e
ss
fi
x
ed
b
u
g
t
h
at cause
d
a segv
when
s
ne
w
failed
commit
|
commitdiff
|
tree
2010-08-10
B
erk H
e
ss
rem
o
ved
C
YS2 fr
o
m the Am
b
e
r rtp
fi
l
es
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
r
e
moved pdb2gmx -cysh hidden option that
s
hould have
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk H
e
ss
made mdrun -seppot
w
ork wi
t
h thre
a
ds an
d
-seppot now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
e
rk Hess
Me
r
ge br
a
n
ch 'release-4-5-
p
at
c
hes' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Be
r
k He
s
s
co
r
recte
d
the
(
irrelev
a
nt) defaul
t
ir->gb_dielectric_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
ad
d
e
d -pbc
o
ption to g_
t
raj
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
read
i
np, used f
o
r e
.
g
.
mdp, no longer
u
ses gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
e
ss
fixed gm
x
_rmpbc
u
ndoing
th
e
shifting when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
s
c
_sigma now als
o
sets the minimum value for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk
He
s
s
make_ndx now allows nearly all ch
a
ra
c
ters in atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
gmxcheck now compar
e
s terms by name
ma
t
ching
commit
|
commitdiff
|
tree
2010-08-04
B
erk
Hess
rem
o
ved
c
ommrec->nthreads fro
m
FAHCORE
code
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
gmxcheck no
w
usi
n
g the
d
iagon
a
l for relative t
o
l
erance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
ess
fixed g_e
n
ergy
m
anual formatting iss
u
es
commit
|
commitdiff
|
tree
2010-08-04
Berk
Hess
grom
p
p automatic ns
t
calcenergy setting
n
o
w
ta
k
e
s s
m
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk He
s
s
adde
d
full p
r
ecision
o
ption to g_traj and
r
e
f
ormat
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
e
rk
Hess
fixed PME commun
i
ca
t
i
on r
a
nge when first DD d
i
m is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
e
rk Hess
made vres
c
ale and Berendsen tcou
p
le work with
V
V, a
l
though
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
correct
e
d LJ on H o
f
cha
r
mm tips3p
commit
|
commitdiff
|
tree
2010-07-29
B
e
rk Hess
completed part
i
al
r
ena
m
e of C
Y
N to CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
co
r
re
c
t
ed the Amb
e
r ami
n
oac
i
ds
.
r2
b
f
iles
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hess
re
n
ame
d
pme_
m
a
x
shift0/1 to pm
e
_maxshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
rep
l
aced the
C
harm
m
vsite parameters (w
h
ic
h
were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hess
corrected a vsite par
a
meter in
t
h
e amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected C
l
atom name in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
a
mb
e
r
ff
a
tomtypes ch
a
nge:
corrected masses
,
re
m
oved
.
.
.
commit
|
commitdiff
|
tree
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