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improved the automatic choice of the number of PME nodes
2010-09-08
Berk Hess
improved
t
he automatic choice of the number
o
f
PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Be
r
k
Hess
added MC
H
3
S
a
tom type
f
or Ch
a
rm
m
fo
r
virtual si
t
es
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
changed the
o
rder
o
f
the o
u
ter loop
s
in t
h
e fft
5
d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
removed emp
t
y edr an
d
xtc files wit
h
nm
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
removed (nan) av
e
rage
printing with
norm
a
l mode
s
commit
|
commitdiff
|
tree
2010-09-07
Berk Hes
s
f
ixed
crash with parallel nm
w
ith cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided creation of neighborlists without j
-
particles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
fixed bug
t
h
a
t c
a
u
s
ed corrupted
c
h
e
c
kpoin
t
files
commit
|
commitdiff
|
tree
2010-08-26
Be
r
k Hess
pd
b
2gm
x
now only allows
a
mism
a
tch of a si
g
n (iso any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk He
s
s
fixed p
d
b2g
m
x
u
s
ing start name
i
s
o end name for
C
-terminus
commit
|
commitdiff
|
tree
2010-08-24
Ber
k
Hess
fixed
b
u
g in search_rt
p
int
r
oduc
e
d
in previous co
m
mit
commit
|
commitdiff
|
tree
2010-08-24
Be
r
k Hess
updated gm
x
_mem
b
ed
.
c
f
o
r
a VV
u
pdat
e
commit
|
commitdiff
|
tree
2010-08-24
B
erk
H
ess
fixed
p
db2gmx behavior fo
r
ne
a
r
l
y
matching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Ber
k
He
s
s
rem
o
ved the pdb2gmx -cwd option and updated the pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
H
ess
pdb2
g
m
x
no
w
print
s
the force field dir be
f
ore the sele
c
tion
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k Hess
fixed mpi hang/c
r
a
s
h with separate pme nodes and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
ess
a
dded function do_cpt
e
_n_
r
eals t
o
checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
es
s
fixed automa
t
ed DD/
P
ME grid d
e
composition
choice which
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk He
s
s
dis
a
bl
e
d
o
p
timized IBM BlueG
e
ne converts2
i
n
ts macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k
Hess
increas
e
d tpx
_
generatio
n
which should have b
e
en done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
en
e
conv now copies t
h
e n
e
w d
e
lta_t e
n
try
commit
|
commitdiff
|
tree
2010-08-20
Berk He
s
s
a
dded dt to energy file frame
s
commit
|
commitdiff
|
tree
2010-08-20
B
e
r
k
H
ess
added free a
n
d som
e
comme
n
t to
deprecated
cl
o
se_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixe
d
segv's
i
n g
_
anaeig
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduced
t
he warning li
m
it for Berend
s
en T-coup
l
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
erk Hess
remov
e
d the bNEMD boolean from the main MD loop
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk
H
ess
a
d
ded some comment to group gromp
p
assignment optio
n
s
commit
|
commitdiff
|
tree
2010-08-18
Be
r
k
Hess
adde
d
group compar
i
son to gmxcheck and pr
i
nt
groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
fixed possible pathe
s
tring buffer over
f
l
o
w in get_libdir
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
added
f
unction r
e
s
c
al
e
_velocities
commit
|
commitdiff
|
tree
2010-08-16
Berk
H
ess
gmx_rmpbc now guesses ePB
C
again for each frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc
g
e
t
s natoms passed again, without natom
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
put omp
p
ragma's in fft5d
.
c between ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
added o
p
enmp pra
g
ma
'
s for the fft5d transp
o
se
routines
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed mdrun write
s
tpidist
.
xvg
o
n a
l
l n
o
des
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixe
d
s
e
gv in mdrun wi
t
h
r
e
p
lica excha
n
ge
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixe
d
f
a
tal
e
rror
i
n mdrun file appending wi
t
h -
m
ul
t
i
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxcheck now prints rmsd's as %g iso
%f
commit
|
commitdiff
|
tree
2010-08-13
B
erk Hess
moved full
precision real
form
a
t defini
t
ion to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk H
e
s
s
reverted
the last,
n
on-
c
osmetic change
to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
minor
c
osm
e
tic
changes in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
mad
e
th
e
p
d
b2gmx occupancy warning more obvious
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
fixed inco
r
rec
t
pd
b
2g
m
x
o
utpu
t
with multiple (a
l
tloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk H
e
s
s
removed -merge fr
o
m
the
pdb2gm
x
manual and
clarified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
fi
x
ed b
u
g that caused a se
g
v when snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
rem
o
ved CYS
2
from the Amber rt
p
fi
l
es
commit
|
commitdiff
|
tree
2010-08-10
B
e
r
k
H
e
ss
remov
e
d
p
db2gmx -cysh hidd
e
n
option that should
h
ave
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Be
r
k
H
e
ss
made mdr
u
n -seppot work with thre
a
ds and -sep
p
ot n
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
M
erge branch
'
release
-
4
-
5
-
p
a
tches' of
git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
erk He
s
s
c
orrected the (ir
r
el
e
vant) de
f
a
u
l
t ir->gb_dielectri
c
_
o
ffset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
r
k Hess
added -pbc option to g_traj
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
r
eadin
p
,
u
sed for e
.
g
.
m
dp, no longer uses gmxcp
p
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
fixed gmx_rmpbc undoing t
h
e shifting w
h
en x!
=
x_s
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hes
s
sc_
s
igm
a
now also sets the minimum val
u
e f
o
r t
h
e soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
ma
k
e_ndx now allows nearly all char
a
cters
i
n a
t
om
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
ess
gm
x
check now compares terms by nam
e
matching
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
removed commrec
-
>
nthreads fr
o
m
FA
H
C
ORE code
commit
|
commitdiff
|
tree
2010-08-04
Berk He
s
s
g
mxchec
k
now
usin
g
the
d
i
a
g
o
n
al for re
l
a
t
i
v
e tolerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hes
s
fixed g
_
energy man
u
al
formatting issues
commit
|
commitdiff
|
tree
2010-08-04
Berk He
s
s
g
r
o
mpp automa
t
i
c n
s
tca
l
c
ener
g
y setting no
w
takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
added full
p
r
e
cision optio
n
to g_traj and reformatted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
fixed PME co
m
mu
n
ic
a
tion range when f
i
rst DD di
m
is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made
vrescale and
Berendsen tcouple w
o
rk
w
ith VV, although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk H
e
ss
co
r
rected LJ
o
n
H of charmm
t
i
ps3p
commit
|
commitdiff
|
tree
2010-07-29
Berk He
s
s
c
om
p
leted pa
r
tial rename o
f
CYN
t
o CYS f
o
r Ambe
r
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
ess
corr
e
cted the Amber aminoacids
.
r2b file
s
commit
|
commitdiff
|
tree
2010-07-28
B
e
r
k He
s
s
ren
a
m
e
d pme
_
maxshift0/1 to pme_ma
x
shift
_
x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
replaced the
C
harmm vsite parameters (which were
O
PLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hess
corre
c
ted a
v
site
parameter in the
amber ff
'
s
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected
Cl atom name in a
m
ber
i
ons
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber ff atomtypes change:
correc
t
ed mas
s
es, remo
v
ed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
u
p
date of ambe
r
03 aminoacids
.
rtp, accide
n
tally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corre
c
t
ed mistak
e
s
in amber03 gbsa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed
typo in Makefile
commit
|
commitdiff
|
tree
2010-07-27
Berk
Hess
moved ff_dum
.
i
tp to
t
he gmx an
d
gromos
ff d
i
rectories
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
corrected
the amber vsite p
a
rameters
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
added his
to
o
p
ls r2b
fi
l
e
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
m
a
de the ff fi
l
e naming of am
b
e
r and charm
m
consi
s
t
e
nt
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
correcte
d
the amber
w
a
t
e
r mode
l
fi
l
es
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
fi
x
ed
PME decomp
o
sitio
n
c
h
eck
for i
n
ver
s
e DD order
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
renamed
a
mber LYP to LYS and changed nam
e
s for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
removed HOH from am
b
er rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k He
s
s
a
dded missi
n
g entries for amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
c
leaned
u
p Amber h
d
b'
s
and add
e
d HO4
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
renamed a
t
om type
s
from a
m
ber99_? etc
.
to
t
he original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fi
x
ed PME co
m
municat
i
on range (no silent
e
rror
s
)
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk
H
ess
removed bui
l
din
g
block RT from the lists in
s
hare/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
d
ded
r
esidu
e
and
a
to
m
r
enam
i
ng
f
or AMBE
R
d
na and rn
a
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added DNA and RNA to the pdb2gmx
.
ar
n
for
m
at
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
rena
m
ed O to O2 in a
m
b
e
r r
n
a
.
r
t
p
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
ed natoms_force_co
n
str to t_fo
r
c
e
rec
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hes
s
renamed
O
to O2
i
n amber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
remov
e
d garbage
f
rom
checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare
)
i
n
c
orrec
t
res
i
due numbers when
u
s
i
ng gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
adde
d
openmm wrapper RF para
m
eter checks
commit
|
commitdiff
|
tree
2010-07-19
Be
r
k Hess
minor upd
a
t
e to t
h
e previos appending f
i
x
commit
|
commitdiff
|
tree
2010-07-19
Berk Hes
s
fi
x
ed
mdr
u
n append check when requ
e
s
t
e
d
out
p
ut
fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hess
added md
p
p
a
ram
e
te
r
for FE dH table
s
commit
|
commitdiff
|
tree
2010-07-05
B
e
r
k
Hess
ch
a
nged th
e
default maximum number of backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
rem
o
v
ed a
l
ot of slow FFT grid size
s
from calc
_
grid
.
.
.
commit
|
commitdiff
|
tree
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