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improved the automatic choice of the number of PME nodes
2010-09-08
Berk He
s
s
i
m
proved the
auto
m
atic
c
hoice of
the nu
m
b
e
r of PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk H
e
ss
added MCH3
S
atom
type for Charmm for virtual s
i
tes
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk H
e
ss
ch
a
nged the order o
f
t
he
out
e
r
l
oops in the fft5d
transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
remo
v
ed empty edr a
n
d
xtc files with nm
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
removed (
n
an) average printing
w
ith n
o
r
m
al modes
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
fixed
crash
w
ith p
a
rallel nm with cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided creation of neighborlis
t
s wit
h
o
u
t j-p
a
rticles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
f
i
xed bu
g
that cau
s
ed
c
orrupted
c
heckp
o
int files
commit
|
commitdiff
|
tree
2010-08-26
Berk H
e
ss
pdb2gm
x
now on
l
y
all
o
w
s
a
mismatch of a sign
(
iso any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixe
d
pdb2gmx us
i
n
g start name iso
en
d
name for C-terminus
commit
|
commitdiff
|
tree
2010-08-24
Berk
Hess
fixed bug in search_rtp introduced
i
n
previous commit
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
upda
t
ed gmx_memb
e
d
.
c
for a V
V
upda
t
e
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
f
i
xed pdb2g
m
x behavior for nearly
m
at
c
hing resi
d
u
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hes
s
removed the pdb2gmx
-cwd option and
updated th
e
pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
B
er
k
Hess
pdb2gmx now p
r
ints the f
o
rce
f
ield
dir
b
efor
e
the
s
election
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
Hess
f
i
xed mpi hang/crash with separa
t
e
p
me
n
ode
s
and d
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk He
s
s
added function do
_
cpte_n_reals to
checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
Hess
fixed automated DD/PM
E
grid decompos
i
tion choice which
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
H
e
s
s
disabled
o
pti
m
ized IBM BlueGene conv
e
r
ts2int
s
macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
ess
increased tpx_genera
t
ion
which should hav
e
been
done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
eneconv
now copies the n
e
w
d
elta_t entry
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
a
dde
d
d
t to energ
y
file frames
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k Hess
added free
and s
o
me comment to depr
e
ca
t
ed
c
lo
s
e_trj
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk H
e
ss
f
i
x
ed s
e
gv's in g_anaeig
commit
|
commitdiff
|
tree
2010-08-18
Berk Hes
s
reduced t
h
e w
a
rn
i
ng
l
imi
t
f
o
r Berendse
n
T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
r
e
moved the b
N
EMD
b
oolean f
r
o
m
the main M
D
l
o
op and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk
Hess
adde
d
some comment t
o
group
grompp ass
i
gnment
opt
i
ons
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
a
dded group comparison to g
m
xcheck and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
f
i
xed possible pathe
s
tr
i
ng
b
uffer ove
r
flow in get_l
i
bdir
commit
|
commitdiff
|
tree
2010-08-17
Be
r
k Hess
added funct
i
on rescale_v
e
locities
commit
|
commitdiff
|
tree
2010-08-16
B
e
r
k
Hess
gmx_rmpbc now guesses ePBC again for each frame
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
gmx_rmpbc gets
n
at
o
ms pa
s
sed
again, withou
t
natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
Hess
put
o
mp pragma's in ff
t
5d
.
c betwee
n
ifdef's
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
add
e
d
openmp pragma's for t
h
e
f
ft5
d
transpose
routines
commit
|
commitdiff
|
tree
2010-08-16
B
erk
H
ess
f
i
xed m
d
run
w
ri
t
es tpidist
.
xvg on
a
l
l no
d
es
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
f
ixed
segv
i
n mdrun with re
p
lica exchange
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed
fatal
e
rror in m
d
run file appe
n
di
n
g
with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxcheck now prints
r
m
s
d's as %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
move
d
full precis
i
on real format de
f
inition to si
m
ple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk
Hess
r
ev
e
rt
e
d t
h
e last, non-
c
osmetic ch
a
nge to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
min
o
r cosmetic
c
hanges i
n
pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk He
s
s
mad
e
t
h
e pd
b
2gmx occupancy warning m
o
re o
b
vious
commit
|
commitdiff
|
tree
2010-08-12
B
erk
H
e
s
s
fixed incorrect p
d
b2g
m
x outpu
t
with multip
l
e
(altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
B
e
rk He
s
s
removed -merge from the pdb
2
gmx man
u
al and clarif
i
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk
H
es
s
fixed
bug that
c
aus
e
d a segv when
s
new faile
d
commit
|
commitdiff
|
tree
2010-08-10
Be
r
k Hess
r
emov
e
d CYS2 f
r
om the A
m
ber
r
tp files
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
remo
v
ed pdb2gmx -cysh
h
idd
e
n
option that
s
h
ould
h
a
ve
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
made mdrun -se
p
pot work wi
t
h thre
a
ds and -seppot now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Be
r
k
He
s
s
Merge
branch 'rele
a
se
-
4-5-p
a
tches'
o
f git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
correcte
d
the (irr
e
le
v
a
n
t
)
d
efault ir
-
>gb_dielectric_offse
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
a
dded
-pbc option to g
_
tra
j
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
readi
n
p
,
used for e
.
g
.
m
dp, no longer us
e
s gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk He
s
s
f
i
xed gmx_rmpbc
un
d
oing the
shifti
n
g when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Be
r
k H
e
ss
sc_
s
igma now als
o
sets
the m
i
nimum
v
a
lu
e
for
the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
m
a
ke_
n
dx now allows nearly al
l
c
haracters in atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
g
mxche
c
k
n
ow compares term
s
by na
m
e
m
atching
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
removed c
o
mmrec->nth
r
eads from FAHCOR
E
code
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
gmxc
h
eck now
u
sing the diagonal for re
l
ative to
l
e
ran
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
fixed g_energy ma
n
ual form
a
tting
issues
commit
|
commitdiff
|
tree
2010-08-04
Berk He
s
s
g
r
o
mpp automa
t
i
c n
s
tc
a
lcenergy settin
g
no
w
t
a
k
e
s
s
m
all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hess
added full
p
recision
option to
g
_tra
j
and reform
a
tted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
erk Hess
fix
e
d PME
c
ommunication range
wh
e
n fir
s
t DD dim
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made
v
rescale and Berendse
n
tcouple work with V
V
, alt
h
ough
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
corrected LJ on H of cha
r
mm tips
3
p
commit
|
commitdiff
|
tree
2010-07-29
Ber
k
Hess
completed par
t
ial
r
enam
e
of CYN to C
Y
S for A
m
b
er
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected the Amber a
m
inoa
c
ids
.
r2b files
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
H
e
s
s
renamed
p
me_max
s
hift0/1 to pme_maxshift_x/
y
commit
|
commitdiff
|
tree
2010-07-28
B
erk Hes
s
replaced t
h
e Charmm vsite p
a
rameters (w
h
ich wer
e
OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k Hess
cor
r
ected a vsite parameter in the
amber ff
'
s
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
correct
e
d Cl a
t
om name in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
B
erk
H
ess
amber f
f
a
t
o
mtypes change: corrected masses, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
u
p
d
a
te of
amber03 amino
a
cids
.
rtp
,
a
ccidentall
y
l
e
f
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
c
orrec
t
ed
m
istakes in amber03 gbs
a
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk
Hess
fixed typo in Makefile
commit
|
commitdiff
|
tree
2010-07-27
B
erk Hess
mov
e
d
f
f_
d
um
.
itp
t
o the g
m
x and gromos ff d
i
rectories
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected
t
h
e amb
e
r vsite parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
added his to
opls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
made the ff file naming o
f
amber and charm
m
consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k Hess
corrected the a
m
ber water model fi
l
es
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed
PME d
e
com
p
osition check
f
or in
v
erse DD order
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed
a
m
b
e
r
LY
P
to LYS and changed names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k
H
ess
removed HOH from amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk
H
ess
added
mis
s
i
ng e
n
tri
e
s for amber rna
.
h
d
b
commit
|
commitdiff
|
tree
2010-07-26
Berk
He
s
s
cle
a
ned
u
p Amber h
d
b's and added HO4
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hes
s
renamed atom types
from amber99_? etc
.
to the
ori
g
inal
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
f
i
xe
d
PM
E
communi
c
at
i
on range
(
no sil
e
nt e
r
rors)
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
mo
v
ed b
u
ilding b
l
ock RT from the l
i
sts in share
/
t
o
p
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
e
d
r
es
i
d
u
e
and atom
renamin
g
fo
r
AMBER dna and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added DNA and RNA to the pdb2g
m
x
.
a
rn forma
t
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
renamed
O to
O2 in amb
e
r rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added n
a
toms_force_constr to
t
_forcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
named O t
o
O
2
in
amber
dn
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
Hess
remov
e
d garbage fr
o
m checkpoin
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
B
e
rk Hess
fixed
(
rar
e
) incorrect residu
e
num
b
ers when using gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
B
e
rk Hess
ad
d
ed op
e
nmm wrapper RF paramete
r
checks
commit
|
commitdiff
|
tree
2010-07-19
Berk
Hess
minor upda
t
e to
the previ
o
s
appending fix
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
fixed m
d
run append check when requested output f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hess
adde
d
mdp paramete
r
for FE dH
t
a
bl
e
s
commit
|
commitdiff
|
tree
2010-07-05
Be
r
k Hess
changed
the
d
e
fau
l
t maximu
m
number
o
f
backups fro
m
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk
H
ess
removed
a
l
o
t
of slow
F
FT grid sizes
from ca
l
c_grid
.
.
.
commit
|
commitdiff
|
tree
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