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removed a lot of slow FFT grid sizes from calc_grid and made calcgrid.c thread safe
2010-07-05
Ber
k
H
e
ss
removed a lot of slow FFT grid
s
izes from calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
documen
t
ed p
u
ll cosine weigh
t
ing
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
renamed mdrun -cptnum t
o
-cp
n
um
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k Hess
added mdrun -cptnum option to keep
a
nd
numb
e
r che
c
kpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
r
e
vert
e
d
accidential
chan
g
e
of
taba
n
g
l
e
s in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk H
e
ss
added include u
p
da
t
e
.
h to coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
d
ded
b
ack const to gmx_sort comp
a
re para
m
s
f
or qso
r
t
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk
H
ess
remo
v
e
d obsolete f
f
tgrid code and disabled PP
P
M with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Ber
k
Hess
c
han
g
ed pdb2g
m
x water model atom c
o
unt d
e
tect
i
on
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
implem
e
nte
d
nsteps=-1 for mdrun
c
ont
i
nuation and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk
H
ess
fi
x
ed small
o
c
.
h
and
s
malloc
.
c definition inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
M
e
rge branch
'
ma
s
ter' of
g
i
t@git
.
grom
a
cs
.
o
r
g:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
removed
s
t
a
tusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed gmx_eneconv
compiler wa
r
nin
g
s
commit
|
commitdiff
|
tree
2010-06-23
Berk Hes
s
fixed ene
c
o
nv -dt optio
n
temporarily n
o
t wri
t
ing av
e
rages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
correc
t
ed edr format issue introdu
c
ed
toda
y
commit
|
commitdiff
|
tree
2010-06-21
Berk
H
e
ss
add gmx_qs
o
r
t routine, since glibc qsort is not
threa
d
s
a
f
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk
Hess
f
ixed typo in fatal_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now mdrun
d
o
es
not
write the trr file when it wo
u
ld
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Be
r
k Hess
added env
v
ar GMX_M
A
XBACKUP
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
fix for the pre
v
i
o
u
s mdrun -rerun c
o
mmit
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
m
d
run -re
r
un now reads t
h
e rerun traj only on the
m
aster
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hess
minor update
f
o
r previou
s
replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fixed mdr
u
n
-
re
r
un giving
N
aN with disp
c
orr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added water mode
l
selection and li
s
t fi
l
e to
pdb
2
g
mx
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
e
ss
ma
d
e a sep
a
rate t
i
ps3p
.
itp file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Mer
g
e branch 'master'
of gi
t
@git
.
gromacs
.
o
r
g
:
gromacs
commit
|
commitdiff
|
tree
2010-06-16
Berk
Hess
added spce to c
h
a
r
mm
2
7
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed MPI cr
a
s
h
when
nat_home=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
resto
r
ed th
e
old order
o
f the mdrun option and
r
emoved
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
repla
c
ed mo
r
e gmx
_
fat
a
l by
c
o
llectiv
e
c
a
lls in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed
a
t
o
m naming in
encad c-termini
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk Hess
with nsteps=-
1
mdrun no
w
p
r
ints ns/day estimate
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
ess
a
d
ded nsteps=-
1
option to mdp_
o
p
t
.
h
tml
commit
|
commitdiff
|
tree
2010-06-16
Berk Hes
s
all
e
nergy m
i
nimizers now do 0 ste
p
s wit
h
nsteps=
0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fi
x
ed incorrect
pdb2gmx CYS2
t
o
C
YS renaming which
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
allvsall loops
now
tr
i
gger particle decompos
i
tion
commit
|
commitdiff
|
tree
2010-06-15
B
e
rk Hess
fatal_er
r
or in the DD initializat
i
on now c
a
lls MPI_Finalize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk H
e
s
s
adde
d
-cwd optio
n
to
p
db2gmx
commit
|
commitdiff
|
tree
2010-06-11
Berk
H
e
ss
fixed mdrun cou
n
ter
resettin
g
i
ssu
e
s
commit
|
commitdiff
|
tree
2010-06-11
Berk Hess
opti
m
ized the number o
f
t
h
r
e
ads
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
m
ade
DD
work pr
o
perly with all non-p
e
riodic system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
added more explanation to idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk
H
ess
fixed uninitialized variable in do_md
commit
|
commitdiff
|
tree
2010-06-10
Ber
k
Hess
fixed par
t
i
c
le decomposition
load
print
commit
|
commitdiff
|
tree
2010-06-04
Ber
k
Hess
f
ixed pdb2gmx mes
s
i
n
g
up
c
oordinates wh
e
n deleting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
B
e
rk Hess
ad
d
ed no
t
es on mdp disre pa
r
ameter
s
commit
|
commitdiff
|
tree
2010-06-03
Berk
Hess
distance restraint ens
e
mble averaging is no longer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
fixed
bug i
n
e
n
um parsing
e
r
r
or message
commit
|
commitdiff
|
tree
2010-06-03
Berk
Hess
a
d
d
ed VV para
m
et
e
rs to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-02
Berk Hess
fixed mor
e
Grom
o
s
atom type name cases
commit
|
commitdiff
|
tree
2010-06-01
Be
r
k He
s
s
clea
n
e
r
fix for atom
t
ype
c
ase issue with GB paramet
e
rs
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixed atom type case issu
e
w
i
t
h
GB paramete
r
s
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixed two G
B
bugs
commit
|
commitdiff
|
tree
2010-05-19
Berk
H
ess
fixed mdrun unwantin
g
ly modifying nstenergy
a
nd
n
s
tlog
commit
|
commitdiff
|
tree
2010-05-18
Be
r
k Hess
impleme
n
t
S
SE exp c
a
l
culation f
o
r
solve_pme
commit
|
commitdiff
|
tree
2010-05-17
Berk Hess
fixed some genborn incl
u
d
e
file detai
l
s
commit
|
commitdiff
|
tree
2010-05-17
Berk He
s
s
reordered pme_solve_yzx
a
rg
u
men
t
s
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
mi
n
or pme_solve virial optimi
z
ation
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
fixed segv
with
m
dr
u
n
-npme 1
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
f
i
xed case of
a
tom
t
ypes in the Gromos for
c
e fields
commit
|
commitdiff
|
tree
2010-05-12
B
e
r
k H
e
s
s
c
o
rrecte
d
pdb2g
m
x force field comments
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
made
a
t
o
m types case sensiti
v
e
commit
|
commitdiff
|
tree
2010-05-11
B
erk Hess
fixed bug
i
n pdb2gmx hdb initialization
commit
|
commitdiff
|
tree
2010-05-11
Berk He
s
s
adde
d
proper DNA
and R
N
A residue recogn
i
t
i
on
commit
|
commitdiff
|
tree
2010-05-11
Berk
Hess
a
dded pro
p
er DNA and RNA
r
esidue recogniti
o
n
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
f
i
xed in
c
o
rrect pdb2gmx
r
esi
d
u
e
n
ame
m
atc
h
i
n
g with
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
B
e
r
k Hess
f
i
x
ed
b
ug with
p
db2
g
mx
a
n
d
mult
i
ple rtp files
commit
|
commitdiff
|
tree
2010-05-11
Berk
Hess
added ch
e
ck for sys/time
.
h e
x
i
stence
commit
|
commitdiff
|
tree
2010-05-11
Berk Hes
s
updated an
d
fine-tuned the coefficients
f
o
r
t
h
e
PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
rem
o
ved in
c
lude of complex
.
h in fft5d
.
h
commit
|
commitdiff
|
tree
2010-05-10
Berk H
e
s
s
f
i
xed
un
d
erallocation in g
m
x_fft_ini
t
_many_1d_
r
ea
l
commit
|
commitdiff
|
tree
2010-05-10
Be
r
k
Hess
fixed name in grom
o
s4
3
a1
.
f
f
Makefile
.
am
commit
|
commitdiff
|
tree
2010-05-10
B
e
rk Hes
s
moved alcohol fi
l
e
s from top to the force f
i
eld s
u
bdirectories
commit
|
commitdiff
|
tree
2010-05-10
B
e
rk Hess
moved alcoh
o
l files fr
o
m
top
to the force field subdir
e
ctorie
s
commit
|
commitdiff
|
tree
2010-05-10
B
erk Hess
c
o
m
pletion of
the
p
db
2
gmx res
i
due renaming
chan
g
e
commit
|
commitdiff
|
tree
2010-05-07
Berk
H
e
s
s
cha
n
g
e
d int
e
rnal Gromacs naming of cys
,
his and
lys
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
added
a
column
f
or single residue chain to r2b f
i
le
commit
|
commitdiff
|
tree
2010-05-07
Ber
k
Hess
fixed segv in grompp whe
n
gmxcpp reports an error
commit
|
commitdiff
|
tree
2010-05-07
Berk
Hess
made grom
p
p
c
harg
e
warn
i
ng
l
e
ss
sens
i
tive to round
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
made
P
ME energy and virial
c
a
l
cu
l
ation opti
o
n
al
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
Merge commit 'origin/2
d
pme'
commit
|
commitdiff
|
tree
2010-05-07
B
erk Hess
rem
o
ved solve
_
x
y
z
commit
|
commitdiff
|
tree
2010-05-07
Berk Hes
s
nstenergy is now -1 by d
e
faul
t
, mea
n
ing nstlis
t
commit
|
commitdiff
|
tree
2010-05-06
B
e
r
k Hess
fixed some
de
t
ails fo
r
nstcalcenergy>1
commit
|
commitdiff
|
tree
2010-05-04
Be
r
k Hess
fi
x
ed
compiler warnin
g
commit
|
commitdiff
|
tree
2010-05-03
Berk Hess
remov
e
d
i
nco
r
rect P
M
E grid
f
actor check
commit
|
commitdiff
|
tree
2010-05-03
Berk Hess
ad
d
ed some e
x
planatio
n
commit
|
commitdiff
|
tree
2010-04-30
Berk H
e
ss
M
e
rge commit 'ori
g
in/master' into
2
dpm
e
commit
|
commitdiff
|
tree
2010-04-30
Berk
H
e
ss
c
orr
e
cted
p
me gather
flop count
f
rom 12 to
6
commit
|
commitdiff
|
tree
2010-04-30
Berk Hes
s
fixe
d
r
est
cycle co
u
nt in serial
commit
|
commitdiff
|
tree
2010-04-30
Berk Hes
s
fixe
d
m
u
lt
i
ple print of r
u
n
termin
a
ti
o
n message
commit
|
commitdiff
|
tree
2010-04-30
Berk
H
ess
fixed seg
v
in energy file
reading
commit
|
commitdiff
|
tree
2010-04-29
Berk
Hess
Merg
e
commi
t
'
origin/master'
into 2dp
m
e
commit
|
commitdiff
|
tree
2010-04-29
Berk Hess
ch
a
nged the PME
p
article communica
t
ion
buffer region
.
.
.
commit
|
commitdiff
|
tree
2010-04-29
Berk He
s
s
fixe
d
posres alloc
a
tion issue
commit
|
commitdiff
|
tree
2010-04-29
Berk Hess
fix
e
d
p
a
rt
i
cles
o
ut of PME
n
ode crash with 2D PM
E
commit
|
commitdiff
|
tree
2010-04-28
Berk
H
e
s
s
fixed the grompp -e option an
d
added note
s
on che
c
kpoint
.
.
.
commit
|
commitdiff
|
tree
2010-04-27
Berk
H
ess
resolved merge con
f
licts
commit
|
commitdiff
|
tree
2010-04-26
B
e
rk Hess
only master mdrun now prints the o
u
tput file renaming
.
.
.
commit
|
commitdiff
|
tree
next