repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
improved the automatic choice of the number of PME nodes
2010-09-08
Be
r
k Hess
improved
t
he automatic choice o
f
the number
o
f
PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk
He
s
s
add
e
d
MCH
3
S atom type
f
or
C
h
armm for virt
u
al sites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
B
erk
H
ess
ch
a
nged the order of the outer loops in
the
f
ft5d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk
H
ess
remove
d
empty edr an
d
xtc file
s
with n
m
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
remo
v
ed (nan) ave
r
age printing with normal mo
d
es
commit
|
commitdiff
|
tree
2010-09-07
Berk He
s
s
fixed crash with
p
ar
a
llel nm
w
ith cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoi
d
ed creation o
f
neigh
b
orlist
s
without j-particles
commit
|
commitdiff
|
tree
2010-08-26
Berk Hes
s
fixed bug that caused corru
p
ted checkpoint
f
iles
commit
|
commitdiff
|
tree
2010-08-26
Berk
Hess
pdb2gm
x
now only allows a
mi
s
m
atch of
a
sign (is
o
any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk
Hess
fixed pdb2gmx using start na
m
e iso end name
for C-terminus
commit
|
commitdiff
|
tree
2010-08-24
Berk
Hess
fixed
bug in search
_
r
t
p introduced in previous co
m
mit
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
u
pdated gmx
_
mem
b
ed
.
c
for a VV updat
e
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixed pdb2g
m
x
b
e
havior fo
r
nearly matching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k Hess
removed the pdb2gmx -cwd
op
t
ion and upda
t
ed the
pdb2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
pdb2gmx n
o
w
prints th
e
force field d
i
r before the s
e
l
ection
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
B
e
rk Hess
fixed mpi hang/cr
a
sh w
i
th separat
e
pme
n
od
e
s
and
dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
Hess
added function do
_
cpt
e
_n_reals to checkp
o
i
nt
.
c
commit
|
commitdiff
|
tree
2010-08-20
B
erk Hess
fixed autom
a
ted DD/P
M
E grid de
c
omp
o
s
i
tio
n
choice which
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
ess
disabled optimi
z
ed IBM B
l
ueGene converts2ints macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
e
s
s
increased tpx_g
e
neration which should have been do
n
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
Hess
ene
c
on
v
n
o
w
copies the n
e
w de
l
ta_t ent
r
y
commit
|
commitdiff
|
tree
2010-08-20
B
erk Hess
added dt to
e
nergy file frames
commit
|
commitdiff
|
tree
2010-08-20
B
erk Hess
adde
d
free and some comme
n
t to deprecated
close
_
t
rj
commit
|
commitdiff
|
tree
2010-08-20
Ber
k
Hess
fix
e
d seg
v
'
s in
g
_
anaeig
commit
|
commitdiff
|
tree
2010-08-18
Be
r
k Hess
reduc
e
d the warning li
m
it fo
r
B
erendsen
T
-
coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
e
r
k
Hess
re
m
oved the b
N
EMD boolean
f
rom th
e
main MD lo
o
p and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added s
o
m
e com
m
ent to gr
o
up grom
p
p assignment o
p
tio
n
s
commit
|
commitdiff
|
tree
2010-08-18
B
erk Hess
added group comparis
o
n
to gmxcheck and print group
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
fi
x
ed possible pathe string buffer ov
e
rflow in get_li
b
dir
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
a
d
ded fu
n
ction res
c
ale_velocities
commit
|
commitdiff
|
tree
2010-08-16
Berk He
s
s
gmx_
r
mpbc
n
ow
g
uess
e
s ePBC again for
e
a
ch frame
commit
|
commitdiff
|
tree
2010-08-16
Berk
H
ess
g
mx_rmpbc
g
ets natoms passed aga
i
n, without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk
Hess
put omp pragma's
i
n fft5d
.
c between ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
added openmp pragma's for the
f
f
t
5d transpos
e
rout
i
nes
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed mdrun writes tp
i
dist
.
xvg on all
n
o
d
es
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed segv in mdru
n
w
i
th rep
l
ica
e
x
c
ha
n
g
e
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fixed fatal e
r
ror in mdrun
file
a
pp
e
nding
w
ith -mul
t
i
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
er
k
Hes
s
gmxcheck now prints rmsd's as %g is
o
%f
commit
|
commitdiff
|
tree
2010-08-13
B
erk Hess
mov
e
d full precisi
o
n real fo
r
mat definition to simple
.
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 Hess
mi
n
o
r cosmetic change
s
in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
B
e
r
k Hess
made
t
he
p
d
b
2gmx oc
c
upancy warning more
o
bvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
fixe
d
incorrect pdb2gmx output with multiple (alt
l
o
c
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
remov
e
d -merge from the pdb2gmx
manual and
clarifi
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ber
k
Hess
fix
e
d
b
u
g
that caused
a se
g
v when
snew faile
d
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
removed CYS2 from the Amber rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk He
s
s
removed pdb2gmx -cysh hidden o
p
tion
th
a
t s
h
ould have
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
ma
d
e mdrun
-
seppot
work with
thre
a
ds and -
s
eppot
n
ow
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
M
e
r
ge
b
ranch '
r
elease-4-5
-
p
atches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
c
orre
c
ted the
(
i
rre
l
e
v
a
nt) default ir->gb_dielectric_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
added -pbc o
p
tion to g_traj
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
re
a
di
n
p,
u
se
d
for e
.
g
.
mdp, no longer uses gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
fixed gmx_rmpbc undoing the
s
h
i
f
t
ing when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
ess
sc_sigm
a
now a
l
so sets
the minimum
v
alue for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
m
ake_ndx
now allo
w
s nearly a
l
l charact
e
rs i
n
atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
gmxcheck no
w
co
m
p
ares
t
er
m
s by
n
a
me mat
c
hing
commit
|
commitdiff
|
tree
2010-08-04
Ber
k
Hess
rem
o
ved commrec->nthreads fr
o
m
F
A
HCORE code
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
g
m
x
c
h
eck now u
s
ing the diagonal for relative t
o
lerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
fixed g_ene
r
gy man
u
al formatt
i
ng is
s
ues
commit
|
commitdiff
|
tree
2010-08-04
Ber
k
Hess
gromp
p
a
uto
m
atic nstc
a
lcener
g
y setting n
o
w takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
added full precision option to g_traj and reformatte
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
H
ess
fixed PME
c
o
m
munication rang
e
when first DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
H
ess
made vrescale and Ber
e
ndsen
tcoupl
e
work with VV, alt
h
ough
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
co
r
rected LJ on H
of c
h
armm t
i
p
s3p
commit
|
commitdiff
|
tree
2010-07-29
Ber
k
H
ess
c
omplet
e
d p
a
r
t
ial renam
e
o
f
C
YN to CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
correc
t
e
d
the A
m
ber amino
a
cids
.
r
2
b
f
iles
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
re
n
amed
p
me_maxshif
t
0/1 to pm
e
_max
s
hif
t
_
x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
replaced t
h
e
C
harmm vsite par
a
meter
s
(which were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hess
correc
t
ed
a
vsite param
e
ter in
the ambe
r
ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
correcte
d
C
l atom na
m
e
in a
m
b
e
r ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber ff
atomtypes
change: correct
e
d
m
asses, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
upd
a
te of amber03 am
i
noacids
.
r
tp, acci
d
ent
a
lly left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected mis
t
akes in amber03 gbsa
.
i
tp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fi
x
ed
typo in
M
akef
i
le
commit
|
commitdiff
|
tree
2010-07-27
B
erk Hes
s
mov
e
d ff_dum
.
itp to the gmx and grom
o
s ff directories
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
correcte
d
the
am
b
er vsite parameters
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hes
s
ad
d
ed his to opls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
m
a
de the ff file naming of amber and charmm consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
corrected the
a
mbe
r
water mo
d
el files
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
f
i
xed PME
d
ecom
p
osition
c
heck
f
or inve
r
se DD ord
e
r
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
named ambe
r
LYP
to
L
YS and
changed
n
ames for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
removed
HOH
f
r
o
m ambe
r
rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
added missing entrie
s
for amb
e
r rna
.
hd
b
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
e
ss
cle
a
ned up Amber hdb's and added HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
named atom types
f
rom amber99_? etc
.
to the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k Hess
f
ixed
P
ME communication range (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
removed buildi
n
g
b
lock
R
T
from
the l
i
sts in
share
/
top
commit
|
commitdiff
|
tree
2010-07-26
Berk
He
s
s
added residue and atom renaming for AMBER
d
na an
d
rn
a
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added DNA and
RNA to the pdb2gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
B
er
k
He
s
s
renamed O to O2 in amber r
n
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
added
n
atoms_force_constr to t_
f
orcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
na
m
ed O to O2 in
a
m
ber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
Hess
r
emoved garbage f
r
o
m ch
e
ckpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Be
r
k Hess
fixed (r
a
re) incorrec
t
residue
nu
m
bers when
using gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
B
erk He
s
s
added openmm
wrapper RF p
a
ram
e
te
r
checks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hes
s
minor u
p
date
t
o the previos appending fix
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
fixed mdrun append check when requ
e
sted outp
u
t fil
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk He
s
s
added
mdp parameter for FE d
H
t
ables
commit
|
commitdiff
|
tree
2010-07-05
B
e
r
k
Hess
changed the
d
efault maximum num
b
er of backups
from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk
Hess
removed a lot of sl
o
w FFT gr
i
d size
s
f
r
om calc_grid
.
.
.
commit
|
commitdiff
|
tree
next