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gmx_rmpbc gets natoms passed again, without natoms many tool could not parse trajecto...
2010-08-16
Berk Hess
g
m
x_rmp
b
c gets nat
o
ms
p
assed a
g
ain, without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
pu
t
omp pr
a
gma's in f
f
t5
d
.
c betwe
e
n ifdef's
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
added openmp pragma's for the f
f
t5d tran
s
po
s
e rout
i
nes
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed mdrun wr
i
t
es tpi
d
ist
.
xvg on
all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
f
ixed segv in mdr
u
n with r
e
plica exchange
commit
|
commitdiff
|
tree
2010-08-16
Berk
Hess
fixed f
a
tal er
r
or in mdrun file appending with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
erk Hess
gmx
c
heck now print
s
r
msd's
a
s %
g
iso
%
f
commit
|
commitdiff
|
tree
2010-08-13
B
e
rk He
s
s
moved fu
l
l precis
i
on real
format def
i
n
i
tion
to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk
Hes
s
reverted the
l
a
s
t, non-cosmetic change
to
p
me
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
min
o
r cosm
e
tic chan
g
es in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
He
s
s
made the pd
b
2gmx occupancy warning more
obvi
o
us
commit
|
commitdiff
|
tree
2010-08-12
Be
r
k Hess
fixed incorrect
pdb2gmx output with multiple
(
a
l
tloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
removed -
m
erge from the pdb2gmx
m
a
n
u
a
l a
n
d cl
a
rified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
f
i
xed
b
ug tha
t
caused a segv when snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
removed CYS2
f
rom the Amber
rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
removed pd
b
2gmx -cysh hidde
n
option that
sh
o
uld have
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
made
mdrun -seppot w
o
rk with t
h
reads a
n
d -seppot
n
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk
H
e
s
s
M
erge branch 'rel
e
ase-4-5-patch
e
s' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Ber
k
Hess
c
orrected the (irrele
v
ant) d
e
fault i
r
->gb_dielectric_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
a
d
d
ed -pbc
o
pti
o
n to g_traj
commit
|
commitdiff
|
tree
2010-08-05
Berk
Hess
readinp,
used for e
.
g
.
mdp,
no longer uses gmxcp
p
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
fixed g
m
x_rmpbc undo
i
ng
t
he shif
t
ing whe
n
x
!
=x_s
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
ess
sc_sigm
a
no
w
also sets
t
he
m
inimum
value for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
ss
make_ndx now
a
llo
w
s
nearly
a
ll cha
r
acters i
n
atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
gmxche
c
k now compa
r
es ter
m
s by
name
m
atch
i
n
g
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
removed
commrec->nthreads
from FAHCO
R
E c
o
de
commit
|
commitdiff
|
tree
2010-08-04
B
erk Hess
gmxchec
k
now using th
e
diagon
a
l for relative toler
a
nc
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk
Hess
fixed g_
e
n
e
rgy
m
an
u
a
l formatting issues
commit
|
commitdiff
|
tree
2010-08-04
B
er
k
Hess
grompp automatic nst
c
alcenergy setti
n
g now takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
e
s
s
added
fu
l
l precision opt
i
on to g_t
r
aj and reformatted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
e
r
k
Hess
fixed PME communica
t
i
on
range wh
e
n first DD dim i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made vrescale and B
e
r
e
ndsen tcouple work
with VV
,
a
lthough
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk H
e
ss
corrected
LJ
o
n H of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Ber
k
Hess
completed partial rename of CYN to CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
c
o
rrected th
e
Amber ami
n
oacids
.
r
2
b files
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
rename
d
p
m
e_maxshift0
/
1 to
p
m
e_maxshift_x
/
y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
re
p
laced
t
he Charmm
vsite parameters (
w
hich
w
ere OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
co
r
rected a vsite para
m
eter
in the ambe
r
ff's
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
H
ess
c
orre
c
ted Cl atom name in amber
ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber ff a
t
om
t
yp
e
s change: corrected masses
,
removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hess
upd
a
t
e
of amber0
3
aminoacids
.
rtp, acci
d
entally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
e
s
s
corr
e
cted m
i
stakes in a
m
ber
0
3 gb
s
a
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
f
ixe
d
typo
in Makefi
l
e
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
mov
e
d ff_dum
.
itp to
t
he gmx and gromos ff
d
i
rectories
commit
|
commitdiff
|
tree
2010-07-27
Berk Hes
s
co
r
r
e
c
t
e
d
t
he amber vsite parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
added his to opls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made th
e
ff file naming of amber and charmm
consis
t
ent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
correc
t
ed the amber water model files
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
fixed PME de
c
om
p
osition c
h
eck for inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k
He
s
s
r
enamed amber LYP to LYS and change
d
names
f
or
water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
removed HOH from amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
add
e
d missing
entrie
s
for amber rna
.
h
d
b
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
cleaned up Amber hdb's
and add
e
d HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
ren
a
med atom types f
r
om amber99_? e
t
c
.
to the ori
g
inal
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed PME
communi
c
ation range (no silent er
r
ors)
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
removed building bl
o
c
k RT from t
h
e lists in share/top
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
added residue and atom
r
enaming for AMBER dna and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
d
ded DNA and RNA to the pdb2gmx
.
a
r
n f
o
rmat
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
re
n
amed O to O2 i
n
a
m
ber rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added n
a
toms_force_constr to
t
_fo
r
cerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
named O
to O2 in amber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
He
s
s
re
m
ove
d
garbage from
checkpoi
n
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
ess
fixed (rare)
inc
o
rre
c
t
r
esidue num
b
ers w
h
en u
s
ing g
m
x_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
add
e
d o
p
enmm wrapper RF param
e
ter c
h
ecks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
minor u
p
date to the
p
revios
a
ppending
fix
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
ess
fixed mdrun append ch
e
ck when request
e
d output
file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hes
s
added mdp parameter for FE dH tables
commit
|
commitdiff
|
tree
2010-07-05
B
e
rk Hess
cha
n
ged the d
e
fault maximum number of backups
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
B
e
r
k
Hess
rem
o
ved a lot of slow
F
FT grid sizes from c
a
l
c
_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
d
o
cumented pu
l
l cosine w
e
ighting
commit
|
commitdiff
|
tree
2010-06-28
Berk
Hess
r
e
name
d
mdrun -
c
p
t
num
t
o -
c
pnu
m
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
e
s
s
added m
d
r
u
n -
c
ptnum
option to keep
a
nd number checkpoints
commit
|
commitdiff
|
tree
2010-06-28
B
e
rk Hess
reverted accidential
c
hange of tabangles in
gromp
p
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Ber
k
Hess
ad
d
ed
inclu
d
e
update
.
h to coupli
n
g
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk He
s
s
adde
d
back co
n
s
t to g
m
x_sort co
m
pare params
f
or qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk
H
e
ss
re
m
oved
obsolete ff
t
g
ri
d
code and d
i
sabled PPPM with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
chang
e
d
p
db2
g
mx water mod
e
l at
o
m
count d
e
te
c
ti
o
n
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
implemente
d
nsteps=
-
1 for mdrun continuat
i
on and
t
p
bconv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
f
i
xed smallo
c
.
h and smalloc
.
c d
e
finit
i
on
i
ncons
i
stencies
commit
|
commitdiff
|
tree
2010-06-24
Berk He
s
s
Merg
e
branch 'master' of git@g
i
t
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k
H
e
ss
removed statusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k Hess
fixe
d
gmx_en
e
conv compiler warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed enec
o
nv -dt
o
pti
o
n
t
em
p
orari
l
y
not writing averages
commit
|
commitdiff
|
tree
2010-06-22
B
e
rk Hess
corre
c
te
d
edr for
m
at i
s
sue introduced today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
a
dd
g
mx_qsort routine, s
i
nce glibc qso
r
t is not
t
h
r
ead
s
afe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typo in fatal_err
o
r call
commit
|
commitdiff
|
tree
2010-06-18
Berk
H
e
s
s
now mdrun does n
o
t write t
h
e t
r
r
file
w
hen it
wou
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Ber
k
Hess
add
e
d
env var GMX_
M
AXBACKUP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fix
for the previous
mdrun
-
r
er
u
n com
m
it
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
mdrun -rerun
now reads
t
h
e rerun traj
o
nly on t
h
e master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
m
i
n
o
r update for pre
v
iou
s
replex bugf
i
x
commit
|
commitdiff
|
tree
2010-06-17
Berk Hes
s
fixed
m
d
r
u
n
-
rerun giving NaN
w
ith di
s
pcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added water model
s
elec
t
ion and list
fil
e
t
o
pdb2
g
mx
commit
|
commitdiff
|
tree
2010-06-17
B
e
r
k
Hess
m
a
de a separate tips3p
.
it
p
file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hess
Merge branch 'master' of git@git
.
g
romacs
.
org
:
g
r
omacs
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
added spce to charmm2
7
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
fixed MPI crash when nat_
h
o
me=0 i
n
DD
commit
|
commitdiff
|
tree
2010-06-16
Berk
Hess
restored the old order
of the mdrun opti
o
n and removed
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
Hess
replaced more g
m
x_fatal by collective
c
a
l
ls in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed atom
n
am
i
ng in e
n
cad c-termin
i
commit
|
commitdiff
|
tree
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