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added DNA and RNA to the pdb2gmx .arn format
2010-07-26
Berk H
e
ss
added DNA and RNA to the pdb
2
gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O to O2
i
n amber
r
na
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
added natoms_fo
r
ce_con
s
tr t
o
t
_
forc
e
rec
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
renamed
O
t
o
O
2 in
am
b
e
r
dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
re
m
oved garbage
from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk
Hess
fixe
d
(
r
ar
e
)
i
ncorrect residue numbe
r
s
when usi
n
g gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
Hess
adde
d
openm
m
wr
a
p
per
R
F pa
r
ameter checks
commit
|
commitdiff
|
tree
2010-07-19
B
e
r
k
Hes
s
minor update to the previos ap
p
e
nding
f
ix
commit
|
commitdiff
|
tree
2010-07-19
B
e
rk Hess
fixe
d
mdrun append
ch
e
ck when r
e
qu
e
sted o
u
tput fil
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk H
e
ss
ad
d
ed md
p
parameter
f
o
r
FE
dH tables
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
c
hanged the default
m
aximum num
b
e
r of backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
rem
o
v
ed a lot
o
f slow FFT grid
size
s
from
calc
_
grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
documented pull co
s
ine we
i
ghting
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
re
n
amed m
d
run -c
p
t
n
u
m t
o
-cpnum
commit
|
commitdiff
|
tree
2010-06-28
Berk
Hess
adde
d
mdrun -cpt
n
um
o
ption to
keep and number checkp
o
ints
commit
|
commitdiff
|
tree
2010-06-28
B
e
r
k
Hess
reverted acc
i
denti
a
l chang
e
o
f
tabangl
e
s in gr
o
mpp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added inclu
d
e
update
.
h t
o
c
o
u
pling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
ess
added back const to gm
x
_
s
o
rt compare para
m
s f
o
r q
s
ort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k Hess
removed obsole
t
e fftg
r
id co
d
e and disabled PPPM
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
cha
n
ged pdb
2
gmx
w
a
ter model atom co
u
nt detection
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
impl
e
mented
n
steps=-1 for mdrun co
n
tinuatio
n
and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed s
m
alloc
.
h a
n
d smalloc
.
c defi
n
ition
i
n
c
o
nsisten
c
ies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge
b
ranch 'master' of git@git
.
gromac
s
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
re
m
ove
d
status
i
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk
H
ess
fixed gmx_eneconv com
p
iler
w
arn
i
ngs
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed
e
neconv -dt opti
o
n temporarily not
w
ri
t
ing
a
vera
g
es
commit
|
commitdiff
|
tree
2010-06-22
B
erk Hess
corre
c
t
e
d edr format issue introduced t
o
day
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
add g
m
x_qsort routine,
si
n
ce glib
c
qsort i
s
not threadsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typo in fatal_error
cal
l
commit
|
commitdiff
|
tree
2010-06-18
Be
r
k Hess
n
ow mdr
u
n does not w
r
ite the tr
r
fi
l
e
when it wou
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
add
e
d
env
v
ar G
M
X_M
A
XBACKUP
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
fi
x
f
o
r the
p
revious mdrun -rerun
commit
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
md
r
u
n -rerun now
r
ead
s
the rerun traj onl
y
on the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
minor update for previous replex b
u
gfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fixed mdrun -reru
n
giving NaN
w
i
th dis
p
c
o
rr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added water model selection
a
nd list file
to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
made a separate
tips3p
.
itp file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hes
s
Merge
b
ranch
'
mast
e
r' of g
i
t@git
.
g
r
omacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
a
d
ded spce
to
charmm
2
7
commit
|
commitdiff
|
tree
2010-06-16
Berk H
e
ss
fix
e
d MPI crash whe
n
na
t
_home=
0
in DD
commit
|
commitdiff
|
tree
2010-06-16
B
er
k
Hess
restored th
e
old order o
f
the mdrun
optio
n
and removed
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Ber
k
Hes
s
rep
l
aced more g
m
x_fatal by
collective calls in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
fixed atom naming in encad c
-
termini
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
wit
h
n
s
teps=-
1
mdrun now prints ns/da
y
est
i
mat
e
commit
|
commitdiff
|
tree
2010-06-16
Berk H
e
s
s
added
n
steps=-
1
o
p
tion to md
p
_
o
p
t
.
htm
l
commit
|
commitdiff
|
tree
2010-06-16
Berk Hes
s
all energy minimizers
now do 0 s
t
eps with nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk He
s
s
f
i
xed incorrect pdb
2
gm
x
C
Y
S2 to
CYS renamin
g
w
h
ich
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
allvsall
l
oops now trigger pa
r
ticle decomposition
commit
|
commitdiff
|
tree
2010-06-15
B
erk Hess
fatal_error in t
h
e DD initialization now call
s
MPI_
F
inalize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk Hess
added -cwd opti
o
n to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
B
e
r
k
H
e
ss
fixed mdrun counter res
e
tting
issues
commit
|
commitdiff
|
tree
2010-06-11
Berk
Hess
optimized
the n
u
mber
o
f threa
d
s
commit
|
commitdiff
|
tree
2010-06-10
B
er
k
Hess
made DD work properl
y
with all non-pe
r
iodic system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
B
erk Hess
added more explanation
to i
d
e
f
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
f
i
x
ed uninitialize
d
v
ariable i
n
do_md
commit
|
commitdiff
|
tree
2010-06-10
Ber
k
Hess
fixed particle decomp
o
sition
l
oad print
commit
|
commitdiff
|
tree
2010-06-04
B
e
rk
Hess
fixed pdb2gmx messing
u
p coordi
n
ates when
de
l
e
ting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added notes
o
n
m
dp disre
parameters
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
distance restraint en
s
emble av
e
raging i
s
n
o
lon
g
er
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
B
e
r
k Hes
s
fi
x
e
d bug
in enum pars
i
n
g
error m
e
ssage
commit
|
commitdiff
|
tree
2010-06-03
B
e
rk Hess
added VV paramete
r
s t
o
mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-02
B
erk He
s
s
fixed more Gromos atom type name
c
ases
commit
|
commitdiff
|
tree
2010-06-01
Berk Hes
s
cleane
r
fix for
a
t
o
m
type case is
s
ue w
i
t
h GB par
a
m
eters
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixed a
t
o
m type case issue with
GB parameters
commit
|
commitdiff
|
tree
2010-06-01
Berk
Hess
fixed two GB bugs
commit
|
commitdiff
|
tree
2010-05-19
Berk Hess
f
ixed
m
drun unwanting
l
y mo
d
ifying nstenergy and nstlog
commit
|
commitdiff
|
tree
2010-05-18
B
e
rk He
s
s
im
p
leme
n
t SSE exp
c
alculati
o
n for so
l
ve_pme
commit
|
commitdiff
|
tree
2010-05-17
Berk H
e
ss
fixed some genborn incl
u
de file details
commit
|
commitdiff
|
tree
2010-05-17
Berk He
s
s
re
o
rde
r
e
d
p
m
e
_s
o
lve_yz
x
arguments
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
minor pme_
s
ol
v
e virial optimization
commit
|
commitdiff
|
tree
2010-05-14
B
erk
H
e
ss
fixed seg
v
wi
t
h
mdrun -np
m
e 1
commit
|
commitdiff
|
tree
2010-05-12
B
e
r
k
Hess
fixed case of
a
tom types in the Gromos
f
o
r
ce fields
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
corrected pdb2gmx force
f
ield comm
e
nts
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
made ato
m
t
ypes
case sens
i
t
i
ve
commit
|
commitdiff
|
tree
2010-05-11
B
e
rk Hess
fixe
d
bug in pdb2gmx
h
d
b initializa
t
ion
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
a
dded proper DNA a
n
d RNA residue
r
ecogn
i
tio
n
commit
|
commitdiff
|
tree
2010-05-11
Be
r
k Hess
adde
d
prop
e
r DNA
a
n
d RNA
r
e
s
idue re
c
ogniti
o
n
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
fixed
incorrect pdb2gmx r
e
sidu
e
name matchi
n
g wit
h
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
ss
f
i
xed bug with
p
db
2
gmx an
d
multiple rtp files
commit
|
commitdiff
|
tree
2010-05-11
Berk H
e
s
s
add
e
d
c
heck f
o
r sys
/
time
.
h
exist
e
nce
commit
|
commitdiff
|
tree
2010-05-11
Ber
k
He
s
s
updated and fine-tuned the coeffi
c
ients
f
or the PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
B
e
rk Hess
removed include
o
f
c
o
m
p
lex
.
h
i
n fft5d
.
h
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
fixed underallocation in
g
mx_fft_init_many_
1
d_rea
l
commit
|
commitdiff
|
tree
2010-05-10
Berk Hes
s
fixed name in grom
o
s4
3
a
1
.
ff M
a
kefile
.
am
commit
|
commitdiff
|
tree
2010-05-10
Be
r
k Hess
moved
a
lcohol files from top to t
h
e forc
e
field subdirector
i
es
commit
|
commitdiff
|
tree
2010-05-10
Berk H
e
ss
move
d
alcohol fi
l
es f
r
om top to the force field subdire
c
tories
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
c
ompletion of
t
h
e pdb2gmx
r
esidue r
e
naming
change
commit
|
commitdiff
|
tree
2010-05-07
Berk Hes
s
c
h
anged
i
nternal G
r
o
m
acs n
a
ming of cys, his and lys
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
adde
d
a column for single residue chain to r
2
b f
i
le
commit
|
commitdiff
|
tree
2010-05-07
Berk
H
e
s
s
fixed segv in grompp when g
m
xcpp reports an error
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
made grompp charge war
n
ing less sensitiv
e
to rounding
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
B
e
r
k
Hess
made PME energy
an
d
vir
i
al calcul
a
tion optional
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
Merge commit 'origin/2dpme'
commit
|
commitdiff
|
tree
2010-05-07
Be
r
k He
s
s
removed solve_xyz
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
nsten
e
rgy
is now -1 by defau
l
t, meaning nstlist
commit
|
commitdiff
|
tree
2010-05-06
Berk Hess
fix
e
d some
d
e
tails for nstcal
c
energ
y
>1
commit
|
commitdiff
|
tree
2010-05-04
Be
r
k H
e
ss
fixed
c
om
p
iler w
a
rni
n
g
commit
|
commitdiff
|
tree
2010-05-03
Berk He
s
s
removed
i
nco
r
rect PME
g
r
i
d
factor c
h
eck
commit
|
commitdiff
|
tree
2010-05-03
Berk H
e
s
s
a
d
ded some
e
xplan
a
tion
commit
|
commitdiff
|
tree
2010-04-30
Berk Hess
Merge commit 'origin/
m
aster' into 2dpme
commit
|
commitdiff
|
tree
next