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improved the automatic choice of the number of PME nodes
2010-09-08
Berk
H
ess
i
mproved the automatic choice of
t
he
n
umb
e
r o
f
PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Ber
k
Hess
added
MCH3S atom type
f
or
C
harm
m
for
vir
t
ual
sites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
changed the order of the
o
uter
l
oops in the fft5d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk He
s
s
removed empty edr and
x
tc files with nm
commit
|
commitdiff
|
tree
2010-09-07
Be
r
k
Hess
remove
d
(na
n
)
averag
e
printing with nor
m
a
l
modes
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
fixed
crash with
p
arall
e
l nm w
i
th c
u
t-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided creation
of neighborl
i
sts wit
h
out j-particles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
fixed bug th
a
t caused corr
u
pted check
p
o
int files
commit
|
commitdiff
|
tree
2010-08-26
Berk
He
s
s
pdb2gmx n
o
w o
n
ly allows
a
mi
s
match of a sign (iso
any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixed pdb2
g
mx
u
sin
g
s
tar
t
name iso end name for C
-
ter
m
inus
commit
|
commitdiff
|
tree
2010-08-24
B
erk Hess
fixe
d
b
u
g in search_rtp introduced in prev
i
ous com
m
i
t
commit
|
commitdiff
|
tree
2010-08-24
B
erk Hess
u
p
dated gmx_membed
.
c for
a V
V
update
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixed pdb2gmx beha
v
ior for n
e
arly match
i
ng residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
removed
th
e
pdb2gmx -cwd option and update
d
the pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
pdb2gmx n
o
w prin
t
s the
f
orce field
d
i
r before the selection
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k Hess
fixed mpi hang/crash with separate pme nodes
and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added f
u
n
ction do_cpte_
n
_reals to checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
B
er
k
H
es
s
fixed
a
utomated DD/PME grid decompo
s
ition choic
e
w
h
ich
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
disabled optimized
IBM BlueGene c
o
nver
t
s2
i
nt
s
macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
Hess
increas
e
d t
p
x_g
e
n
eration which should have been done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
eneconv n
o
w copies the new delta_t entry
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
ess
adde
d
dt to ene
r
gy file frames
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added free and som
e
comment to deprecated
c
l
ose_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fi
x
ed segv
'
s
in g_anae
i
g
commit
|
commitdiff
|
tree
2010-08-18
B
e
rk H
e
ss
reduced the warning limit f
o
r Ber
e
ndse
n
T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
rem
o
ved the b
N
E
M
D bo
o
l
ean from the ma
i
n MD
loop and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added some comment to
gro
u
p gromp
p
a
s
signment optio
n
s
commit
|
commitdiff
|
tree
2010-08-18
Berk
H
e
ss
ad
d
ed g
r
oup comparison to
gmxcheck
and print
g
roups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
fixed possible
path
e
st
r
ing
b
uff
e
r overflow
in get_l
i
bdir
commit
|
commitdiff
|
tree
2010-08-17
Ber
k
H
e
ss
added funct
i
on re
s
c
ale_vel
o
cities
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc
now guesses e
P
BC aga
i
n for each f
r
ame
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
Hess
gmx_rm
p
b
c
g
e
ts
natoms passed
again, without n
a
toms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
put omp pra
g
ma's in fft5d
.
c
be
t
ween ifde
f
'
s
commit
|
commitdiff
|
tree
2010-08-16
Berk He
s
s
added o
p
enmp pragma's for the fft5d transpose routines
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fixed mdrun writes
tpi
d
ist
.
xvg
on
all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk He
s
s
f
ixed se
g
v in m
d
run with re
p
lica exchang
e
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
He
s
s
fixed fatal
error
i
n m
d
run file
a
ppend
i
ng with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
e
rk Hes
s
gmxcheck now prints r
m
s
d's as %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk
H
ess
moved
full
precis
i
o
n
real fo
r
mat
d
efinition
t
o sim
p
le
.
h
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
reverted the last, non
-
co
s
meti
c
change to p
m
e
.
c
commit
|
commitdiff
|
tree
2010-08-12
B
e
r
k Hess
minor cosmetic cha
n
ges i
n
pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
ma
d
e the pdb2gmx occupancy
warn
i
n
g
more obvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
fixed
i
n
c
orre
c
t pdb
2
gmx output
w
ith multiple (alt
l
o
c
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk
Hes
s
rem
o
ved -mer
g
e
fr
o
m the pdb2g
m
x manual and
c
larified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hes
s
fixed bug that caused a segv
w
he
n
snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
remove
d
CY
S
2 fr
o
m
the Amber rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk He
s
s
r
emove
d
pdb2gmx
-cys
h
hid
d
en option that should have
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk
H
ess
m
ade md
r
un -se
p
pot work with thread
s
a
nd
-seppot now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
Merge b
r
anch '
r
ele
a
s
e
-4-5-
p
atc
h
es' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk
H
ess
corrected the (irrelevant)
default ir->gb_dielectric
_
o
f
fset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
es
s
added -pbc opt
i
on
to g_traj
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
r
e
adinp,
u
sed
f
or e
.
g
.
mdp
,
no long
e
r uses g
m
xcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
fixed
gmx_rmpbc und
o
ing the shift
i
n
g
when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
B
erk Hess
s
c_s
i
gma now
also
s
ets
the minimum va
l
ue for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
make_
n
dx n
o
w allows near
l
y all
chara
c
ters in atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
s
s
g
m
xcheck now compares te
r
ms by name matching
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
removed
c
ommrec->nthre
a
ds from
FAHCORE co
d
e
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
gm
x
check no
w
u
sin
g
t
h
e diagonal
f
or relative
t
oler
a
nce
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk H
e
ss
fixed g
_
energ
y
m
a
nu
a
l formatting issues
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
grompp automatic nstcalce
n
ergy setting now takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Ber
k
He
s
s
added full precision option
to
g_
t
raj and reform
a
t
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
f
i
xed P
M
E communi
c
ation range when first DD di
m
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk H
e
ss
made vr
e
s
c
ale and
B
erendsen t
c
ou
p
le work wi
t
h VV
,
although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk
H
ess
corrected LJ on H of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk Hess
complet
e
d
parti
a
l rename of CYN to CY
S
fo
r
Amber
commit
|
commitdiff
|
tree
2010-07-28
B
erk Hess
corrected the Amber aminoac
i
ds
.
r
2b files
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
renam
e
d
pm
e
_
m
ax
s
hift0
/
1 to p
m
e_maxsh
i
ft_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
r
e
p
laced the Charmm vs
i
te parameters (which were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected a vsite
parameter in the
amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
c
orrec
t
ed
Cl atom name in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk H
e
ss
a
m
b
er ff atomtypes change: co
r
rected masse
s
,
removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
erk Hes
s
update of amber03 aminoacids
.
rtp,
a
cci
d
entally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
e
ss
c
orrecte
d
mis
t
akes
i
n
a
m
ber
0
3 g
b
sa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
f
i
xed typo in Makefile
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
moved ff_dum
.
itp to the
g
m
x
and gromos ff directo
r
ies
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
corrected the amber vsite p
a
rameters
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
a
dded h
i
s to o
p
ls r2
b
file
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
H
e
ss
made the ff file naming
of amber an
d
charmm consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
correct
e
d the amber wate
r
mode
l
files
commit
|
commitdiff
|
tree
2010-07-27
Berk He
s
s
fix
e
d PME decomp
o
sit
i
on che
c
k fo
r
inverse D
D
order
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
r
e
named a
m
ber
LYP t
o
LYS
and changed
names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
removed HOH
f
rom amb
e
r r
n
a
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
d
ded missing
e
ntries
f
o
r amber
r
na
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
cleaned up
A
mber hdb's and
a
dded
H
O4
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ren
a
med at
o
m ty
p
es fro
m
amb
e
r9
9
_? etc
.
t
o the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
fixed
P
ME co
m
muni
c
ation range (no sil
e
nt
erro
r
s)
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k
Hess
removed build
i
ng b
l
ock RT fr
o
m
the lists in share
/
top
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k Hess
ad
d
ed
residue an
d
a
t
om r
e
naming for A
M
B
E
R dna an
d
rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added DNA a
n
d RNA to the pdb
2
gm
x
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
renamed O t
o
O2 in amber rn
a
.
r
tp
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k He
s
s
added natoms_force_
c
onstr
t
o t_forcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O
t
o
O2 i
n
a
mber
d
na
.
r
t
p
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
Hess
remove
d
g
arbage fro
m
c
h
eckpo
i
nt
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare) incorrect residu
e
n
u
m
b
ers when
u
s
ing gmx_mto
p
_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Be
r
k H
e
ss
a
d
ded openmm wr
a
pp
e
r
R
F
p
arameter checks
commit
|
commitdiff
|
tree
2010-07-19
B
e
r
k
Hess
minor
up
d
ate to th
e
prev
i
os appending f
i
x
commit
|
commitdiff
|
tree
2010-07-19
Berk
Hess
fixed mdrun app
e
nd che
c
k when requested output
file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hess
ad
d
ed
mdp parameter for FE
d
H tables
commit
|
commitdiff
|
tree
2010-07-05
Be
r
k
H
ess
changed the d
e
fau
l
t maxim
u
m num
b
e
r of backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
B
e
rk Hess
re
m
oved a lot of slow FFT
g
rid sizes from cal
c
_grid
.
.
.
commit
|
commitdiff
|
tree
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