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removed (nan) average printing with normal modes
2010-09-07
Be
r
k Hess
remo
v
ed (nan) average printi
n
g with normal modes
commit
|
commitdiff
|
tree
2010-09-07
Berk H
e
ss
fixed c
r
ash wi
t
h parallel nm with cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided c
r
eat
i
on of
n
e
ighborlists without j-particles
commit
|
commitdiff
|
tree
2010-08-26
Be
r
k Hess
fixed bug that caused corrupted checkpoint files
commit
|
commitdiff
|
tree
2010-08-26
Berk Hes
s
pdb2gmx now on
l
y
allows a mis
m
atch
o
f a sign (
i
so any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
fixed pd
b
2gm
x
us
i
ng start name iso end name
f
or
C
-te
r
min
u
s
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
fix
e
d b
u
g in search_rtp
i
ntroduced
i
n previous commit
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
update
d
gmx_membe
d
.
c for a VV up
d
a
t
e
commit
|
commitdiff
|
tree
2010-08-24
Ber
k
Hess
f
i
xed pdb2gmx behavior f
o
r nearly match
i
ng
residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
rem
o
ved
the pdb
2
gmx -cwd option and updated
t
he pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
Hess
pdb2gmx now print
s
the force field dir before
t
he selection
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk
H
ess
fixed mpi
hang/cr
a
sh
with se
p
ara
t
e pme
nodes and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added function do_cpte_n_reals t
o
checkpoint
.
c
commit
|
commitdiff
|
tree
2010-08-20
B
e
rk
Hess
f
i
x
ed
a
utomated
D
D/PME gr
i
d decompos
i
t
ion choice which
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
di
s
abled opti
m
i
z
ed IBM B
l
ueGe
n
e converts2ints macr
o
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
incr
e
a
s
ed tpx
_
generation which should have be
e
n d
o
ne
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
B
erk Hess
eneconv now
c
opi
e
s the n
e
w delta_t entry
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added dt t
o
energy
f
ile frames
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
added
f
ree and some commen
t
to deprecated close_t
r
j
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
fixed segv's in g_anaei
g
commit
|
commitdiff
|
tree
2010-08-18
B
erk Hess
reduced th
e
war
n
i
ng
l
im
i
t for Berendsen
T
-coupl
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
e
r
k
Hess
removed t
h
e b
N
EMD
boolea
n
from the
m
ain MD loop and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
e
r
k Hess
add
e
d some comment
to group
g
rompp assignment options
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
add
e
d group comparison
t
o gmxcheck and pr
i
nt
g
roups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Be
r
k
Hess
f
i
xed po
s
sible pat
h
e string b
u
ffer overflow in ge
t
_libd
i
r
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
a
d
ded
function re
s
cale_velocitie
s
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k
Hess
gmx_rmpbc now g
u
esses
eP
B
C again for each fram
e
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
g
mx_rmpbc gets natoms p
a
s
s
ed again, wi
t
hout natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
put omp pragma
'
s in fft5d
.
c b
e
tween ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
a
d
ded openm
p
prag
m
a's
for the
f
ft5d transpose routines
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
Hess
fix
e
d
m
drun
w
rites tpidi
s
t
.
x
vg on
a
ll
no
d
es
commit
|
commitdiff
|
tree
2010-08-16
Berk Hes
s
fixed
segv
in mdru
n
with rep
l
ica
exch
a
nge
commit
|
commitdiff
|
tree
2010-08-16
Berk
He
s
s
fixed fatal error
i
n mdrun file appending with -
m
ulti
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxche
c
k now prints
r
ms
d
's
a
s %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Ber
k
Hess
moved full p
r
ec
i
sion real format d
e
fin
i
tio
n
to s
i
mple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
reve
r
ted the last, non-cosmetic change to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk H
e
ss
minor cosmetic
changes
in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
made the pdb2gmx occup
a
ncy warnin
g
mor
e
ob
v
ious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
fixe
d
incorrect pdb2gmx o
u
tput with multiple
(
altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk
H
ess
re
m
oved -merge f
r
om the pdb2gmx manual and
c
larified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
f
i
x
ed bug that
c
aused
a
s
egv whe
n
sne
w
f
ail
e
d
commit
|
commitdiff
|
tree
2010-08-10
Berk
H
ess
removed CY
S
2 from th
e
Am
b
e
r rtp files
commit
|
commitdiff
|
tree
2010-08-10
B
e
rk Hess
remove
d
pdb2gmx -cysh hidden op
t
ion that sho
u
ld
ha
v
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Be
r
k Hess
made mdrun
-
s
eppot wor
k
w
i
th t
h
reads and -seppot
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
e
rk
Hes
s
Merge branch 're
l
ease-4
-
5-pat
c
hes'
o
f
g
it
@
git
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
e
r
k Hes
s
corrected
t
he
(i
r
relevant)
default ir->gb
_
die
l
ectr
i
c_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
added -pbc option to g_tra
j
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
readinp, used f
o
r e
.
g
.
md
p
, no longer uses gmx
c
pp
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
f
ixed gmx_
r
mpbc
undoing the shifti
n
g
when x!=x
_
s
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk He
s
s
sc_si
g
ma now also sets
t
he mini
m
um
value
f
o
r the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
ma
k
e_ndx no
w
allo
w
s nearly a
l
l chara
c
ters
i
n atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
gm
x
check now comp
a
res terms
by name
m
atching
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
ess
rem
o
ved commrec-
>
nthreads from FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hes
s
gmxcheck now
u
sing the
diagonal for relative
toleran
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
fixed g_energy ma
n
ual
formatting iss
u
e
s
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
grom
p
p
a
utomatic
nstca
l
c
e
ner
g
y setti
n
g now
t
akes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
a
dded full precision option to
g_traj an
d
reforma
t
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
fi
x
e
d PME co
m
munication range when fi
r
s
t
DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
erk
Hess
ma
d
e
v
rescale and
B
e
r
endsen
t
c
ouple
w
o
r
k with
VV, a
l
thoug
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
correcte
d
L
J on H
of charmm
t
ips
3
p
commit
|
commitdiff
|
tree
2010-07-29
B
erk Hess
comp
l
eted partial rename of CYN to CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k
Hess
correc
t
ed the Amber
a
m
inoacids
.
r2b fi
l
es
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
r
e
n
amed pme_
m
a
xshift0/1 to
p
me
_
maxshift
_
x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
r
e
p
laced the Ch
a
rmm vsite para
m
e
t
ers (whic
h
were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
ess
c
orre
c
t
e
d a vsite parameter
in the
a
mber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
c
orrec
t
ed Cl atom name in amber ions
.
it
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
amber
f
f
at
o
mtypes change: corre
c
ted mass
e
s, remo
v
ed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
erk
Hess
update of amber03
a
m
i
noacids
.
rtp,
a
ccidentally l
e
ft
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk
He
s
s
corrected m
i
stakes in
a
m
ber0
3
gbsa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
fixed typo in
M
a
kefile
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
moved ff_dum
.
itp
t
o
the
gmx and gromos ff di
r
ect
o
ries
commit
|
commitdiff
|
tree
2010-07-27
Berk
Hess
co
r
rect
e
d the amber
vsite par
a
meters
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
adde
d
his to o
p
ls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
mad
e
the ff file na
m
ing
o
f
ambe
r
and
c
ha
r
mm consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
erk Hess
corre
c
ted
t
he
amber water mode
l
f
i
l
es
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PME
d
e
com
p
o
si
t
i
on check for
inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
B
er
k
Hess
renamed ambe
r
LY
P
to LYS and c
h
an
g
ed names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk H
e
ss
remov
e
d
H
OH from amber rn
a
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
added
m
i
s
s
ing e
n
tries for
amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
cleaned up Amber hd
b
's a
n
d a
d
ded HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
en
a
med
a
tom types
from amber99_? etc
.
to the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed PME commun
i
cation
range (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
re
m
oved buildin
g
block RT from
t
he l
i
sts
i
n
sha
r
e
/
top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added residue and
atom renaming
for AMBER
d
n
a and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
added
DNA and RNA to the pdb2gmx
.
arn form
a
t
commit
|
commitdiff
|
tree
2010-07-26
B
erk He
s
s
renamed O to O2 in amber rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
d
d
e
d natoms_force_const
r
to t_for
c
erec
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
r
e
named O
t
o O
2
in
a
mbe
r
dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
removed
g
arbage from checkpo
i
nt
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
f
ixed (rare) inc
o
rre
c
t
residue
n
u
mbers
w
h
en u
s
ing gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk H
e
ss
added openm
m
wrapper R
F
parame
t
er checks
commit
|
commitdiff
|
tree
2010-07-19
Ber
k
Hess
minor update to
t
h
e previ
o
s
a
p
pending f
i
x
commit
|
commitdiff
|
tree
2010-07-19
Berk Hes
s
f
i
x
ed mdr
u
n
a
ppend c
h
eck when
r
eques
t
ed outp
u
t f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hess
ad
d
e
d
mdp p
a
ram
e
ter for F
E
dH tables
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
changed
t
h
e
default ma
x
i
mum num
b
er of backups
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk He
s
s
removed a lot of slow FFT grid
s
i
zes
fro
m
calc
_
grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk
Hess
docu
m
e
n
ted
pull
c
osine weighting
commit
|
commitdiff
|
tree
2010-06-28
Berk
Hes
s
r
en
a
med
mdrun
-
cptnum t
o
-cpnum
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added mdrun -cptnum option t
o
ke
e
p and number
checkpo
i
nts
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
r
e
verted accidential cha
n
ge of tabangl
e
s in
g
r
ompp
.
.
.
commit
|
commitdiff
|
tree
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