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added some comment to group grompp assignment options
2010-08-18
B
erk Hess
added some comment to gro
u
p
g
rompp assignment options
commit
|
commitdiff
|
tree
2010-08-18
Be
r
k He
s
s
added
group com
p
arison
t
o
gmxch
e
ck
a
nd
print group
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
erk Hess
fixed possible
p
athe string buffer overflow in
g
e
t
_
l
i
b
dir
commit
|
commitdiff
|
tree
2010-08-17
Ber
k
Hess
added
f
unction resc
a
le_ve
l
ocitie
s
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc
now g
u
es
s
es ePBC again for each f
r
a
me
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc get
s
natoms
pa
s
sed
again, with
o
u
t
natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
put omp p
r
agma's
i
n
fft5d
.
c between ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
added ope
n
mp
p
ragma's for the
fft5d trans
p
os
e
routines
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fixed md
r
un writes
tpidist
.
xvg on all nodes
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
Hess
fixed segv
i
n
mdrun wit
h
re
p
li
c
a
exchan
g
e
commit
|
commitdiff
|
tree
2010-08-16
B
erk Hess
fix
e
d fatal error in m
d
run file appendi
n
g with -mul
t
i
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxcheck
n
o
w prints rmsd's as %g i
s
o %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
moved
full precision real format
definit
i
on
t
o
simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
reverted the l
a
st, n
o
n-cosme
t
i
c
ch
a
ng
e
to
p
me
.
c
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
He
s
s
m
i
n
or
c
osm
e
tic c
h
anges
i
n pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk
H
ess
m
ade the pd
b
2gm
x
occupancy warning
more obv
i
ous
commit
|
commitdiff
|
tree
2010-08-12
B
er
k
Hess
fixed incorrect
p
db2gmx output wi
t
h mu
l
tiple (a
l
tloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
r
em
o
ved -merge from
t
he pdb2gmx manual and c
l
arified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk H
e
s
s
fixed bug t
h
at caus
e
d
a se
g
v w
h
en snew fai
l
ed
commit
|
commitdiff
|
tree
2010-08-10
Berk
He
s
s
removed
CY
S
2 from the Amber rtp
f
iles
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
removed pdb2gmx -cysh hidden option
t
hat should
h
ave
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
B
erk Hes
s
m
a
d
e
mdr
u
n -seppot
work wi
t
h threads an
d
-sepp
o
t
n
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
Merge branch 'r
e
lea
s
e-4-
5
-patches
'
of git
@
g
it
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
c
o
rrected the (irrelevant
)
defa
u
lt
i
r
->gb_dielectric_offse
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
added -pbc option t
o
g_traj
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
H
e
s
s
readi
n
p, use
d
for e
.
g
.
mdp, no longer uses g
m
x
c
pp
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
fixed
g
mx
_
rmpb
c
u
n
doing the shifting when x!=x_
s
commit
|
commitdiff
|
tree
2010-08-05
Be
r
k
Hess
s
c_sigma no
w
a
l
so sets the
minimum
value for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
m
a
ke_
n
dx
no
w
allows n
e
arl
y
all ch
a
racte
r
s
i
n atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
gm
x
c
h
eck
n
ow c
o
mpare
s
terms by name
m
a
tch
i
ng
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
ess
removed commrec->nt
h
reads fr
o
m FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hess
g
mxcheck now using
the diagonal for relative toleran
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
f
i
xed g
_
energy m
a
nual
f
ormatting issu
e
s
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
grompp a
u
tomatic nstcalcenergy set
t
ing now
takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk
Hess
a
d
ded
full precisi
o
n
o
p
tion to g_traj
and reformat
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
f
ixed PME communica
t
i
o
n ra
n
ge when fir
s
t DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
Hes
s
made vrescale and B
e
rend
s
en tc
o
uple
w
or
k
with VV, although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk
Hess
corr
e
cted LJ on H of cha
r
mm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk
Hess
completed partial re
n
am
e
of C
Y
N to
C
YS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corre
c
ted the Amber
a
minoacids
.
r2b fi
l
es
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
r
ena
m
ed pme_
m
ax
s
hift0/
1
to pme_maxshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
replac
e
d
the Charm
m
vsite paramet
e
rs (w
h
ic
h
were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k Hess
corrected a
v
s
ite parameter in the a
m
b
er ff
'
s
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k
Hes
s
c
o
r
r
ected Cl atom name in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk H
e
ss
amber ff atomtyp
e
s
c
hange
:
cor
r
ected mas
s
es, remov
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
up
d
ate of amber03 a
m
inoacids
.
rtp, accidentall
y
left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk He
s
s
corrected mist
a
k
es in amber03 g
b
sa
.
i
tp
commit
|
commitdiff
|
tree
2010-07-27
B
erk
H
e
ss
fixed
t
ypo in Makefile
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
mo
v
e
d
ff_dum
.
itp to t
h
e gmx and g
r
omo
s
ff
directo
r
ies
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k
Hess
corrected the
a
mber
v
sit
e
p
aramete
r
s
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
added h
i
s
to opls r2b file
commit
|
commitdiff
|
tree
2010-07-27
B
erk
H
ess
made the ff fil
e
naming
o
f amber
a
nd charmm
c
onsistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
c
o
r
rected
t
he amber water
m
odel files
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
f
ix
e
d PME decomposit
i
on
check for invers
e
D
D
o
rder
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed
amber LYP to LYS and change
d
na
m
e
s
for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
removed HOH from amber rna
.
hd
b
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added
m
issing entri
e
s
for amber rn
a
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
cl
e
a
n
ed up A
m
be
r
h
d
b's
a
nd added HO4
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
r
e
named atom types from
a
mbe
r
99_? etc
.
to the o
r
igi
n
al
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
f
i
x
e
d PME c
o
mmunication ran
g
e (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
remove
d
bu
i
lding blo
c
k R
T
from the lists in sh
a
re/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added residue and atom renaming for
A
MBER dn
a
and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
adde
d
DN
A
and RNA to
t
h
e
pdb2gmx
.
ar
n
form
a
t
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
renamed O to O2 in amb
e
r
r
na
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k
Hess
a
d
ded natoms_force_cons
t
r to t_
f
o
rcer
e
c
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O t
o
O2 in
a
mber dn
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
r
emoved
g
arbage from checkp
o
i
n
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk
Hess
fixed
(rar
e
)
i
n
correct
r
esidue numbers when
using
g
m
x
_
m
t
op_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
adde
d
openmm wrapper RF paramete
r
ch
e
cks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
m
inor update t
o
th
e
pre
v
ios ap
p
e
n
ding fix
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
e
ss
f
ixed mdrun ap
p
e
n
d check
when requested outpu
t
fi
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk
Hess
added mdp parameter
for F
E
d
H tabl
e
s
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
cha
n
ged t
h
e default max
i
mum number of backups
f
r
om
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk He
s
s
re
m
oved a lot
o
f
slow FFT grid siz
e
s
from c
a
l
c
_
g
rid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
documented
p
ull cosi
n
e weig
h
ting
commit
|
commitdiff
|
tree
2010-06-28
Ber
k
Hess
renamed md
r
u
n -cptnu
m
to -cpnum
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
ad
d
ed
m
d
run -cptnum option t
o
keep and nu
m
ber checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted accidential change of ta
b
a
n
gles in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
e
r
k
Hess
added include
update
.
h t
o
coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added
back const to gmx_s
o
rt compare
p
arams f
o
r qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
removed
ob
s
ol
e
te fftgrid co
d
e
and dis
a
bled
PPPM with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
cha
n
g
e
d
p
d
b
2g
m
x
water model
at
o
m
count de
t
e
ction
commit
|
commitdiff
|
tree
2010-06-24
Berk H
e
ss
implemented
n
steps=-1 for mdr
u
n
con
t
inua
t
ion and
tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fi
x
ed small
o
c
.
h and smalloc
.
c definiti
o
n
inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge br
a
nch 'mast
e
r
'
of git@git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
re
m
oved st
a
t
u
s
i
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
B
e
rk
H
es
s
f
i
xed gmx_e
n
econv compiler
warnings
commit
|
commitdiff
|
tree
2010-06-23
B
e
rk Hess
f
ixed eneconv -d
t
o
ptio
n
tempo
r
a
r
ily not w
r
iting averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
cor
r
e
c
t
e
d edr format issu
e
introduced today
commit
|
commitdiff
|
tree
2010-06-21
B
e
rk Hess
a
d
d
gmx_qsort rout
i
ne, since glibc qsort is
n
ot thre
a
dsa
f
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Ber
k
Hess
fixed ty
p
o in fatal_error
c
all
commit
|
commitdiff
|
tree
2010-06-18
B
e
rk
H
ess
now
m
drun
d
oes not write
t
he trr f
i
le when it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk
Hess
a
d
d
e
d e
n
v var GMX_MAXBACKUP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
f
ix for the pr
e
vious mdrun -reru
n
commit
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
m
drun -
r
erun now reads
t
he rer
u
n t
r
aj
only
o
n
the
master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk
Hess
minor upda
t
e for previous r
e
plex
bugfix
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
H
e
s
s
fixed mdrun -rerun gi
v
i
ng NaN w
i
th dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
add
e
d wa
t
er model selection and list fil
e
to pdb
2
gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk Hes
s
made
a s
e
para
t
e tips3p
.
itp file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk
Hess
M
erge branch 'master' of git@gi
t
.
gromacs
.
org:
g
romac
s
commit
|
commitdiff
|
tree
next