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added some comment to group grompp assignment options
2010-08-18
B
erk Hes
s
added some comment
t
o grou
p
grompp assignment options
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
a
d
ded group
compa
r
ison to
g
mxchec
k
and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk
Hess
fixed possi
b
le
p
athe string
buffer
o
v
erflow
in get_
l
ibdi
r
commit
|
commitdiff
|
tree
2010-08-17
B
erk Hess
added function
r
esca
l
e_veloci
t
ies
commit
|
commitdiff
|
tree
2010-08-16
B
e
r
k
H
es
s
gmx_rm
p
bc now guesses ePBC a
g
ain f
o
r
each
frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gm
x
_
r
mpbc gets natoms passed aga
i
n, wit
h
out natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
put omp pragma's in ff
t
5d
.
c be
t
w
een
i
fdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk He
s
s
ad
d
ed openmp pra
g
ma
'
s
f
o
r
the f
f
t5d t
r
anspo
s
e routines
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
f
ixed mdrun w
r
ites tpidist
.
xvg on all nodes
commit
|
commitdiff
|
tree
2010-08-16
B
erk
H
e
ss
fixed segv i
n
mdrun with replica exch
a
nge
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
fix
e
d f
a
tal
e
r
r
o
r in mdrun file app
e
nding
w
ith -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
e
r
k Hess
gmxc
h
eck now pri
n
ts r
m
sd's as %g i
s
o
%
f
commit
|
commitdiff
|
tree
2010-08-13
Berk He
s
s
moved full precision real form
a
t
d
efinition to
s
imple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
reverted
the last,
n
o
n-cosmetic change t
o
pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk
Hess
min
o
r
cosmetic
ch
a
nges
i
n pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
made the pdb2gmx oc
c
u
p
ancy
warnin
g
more obvi
o
us
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
fixed inc
o
rr
e
ct
pdb2gmx output wi
t
h mul
t
iple (altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ber
k
Hess
rem
o
ved
-
merge f
r
om the pdb2gmx manual and clar
i
fi
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
f
i
xe
d
b
u
g that
c
aused a
s
e
gv when snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk Hes
s
re
m
oved CYS2
f
rom
t
he Amber rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
r
e
moved pdb
2
gmx -cysh hidden o
p
tion that
sho
u
l
d
h
a
ve
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
made mdrun
-
s
e
ppot work with thre
a
ds
a
n
d
-seppot no
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Be
r
k H
e
s
s
Merge branch 'relea
s
e-4-5-patches' o
f
git@git
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
c
orrected the (irrelevant) default i
r
->g
b
_dielectri
c
_offs
e
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
a
d
d
e
d
-
p
bc o
p
ti
o
n
to g_traj
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
ss
read
i
np, used for e
.
g
.
md
p
,
no longer u
s
e
s
gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
fixed
g
mx_
r
m
p
bc
undoing the shift
i
ng whe
n
x!=
x
_
s
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
sc_sigm
a
now
also
sets the minimum
v
alue for the s
o
ft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
m
a
ke_ndx now all
o
ws near
l
y all
characters in
atom a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
gmxch
e
ck n
o
w compares
term
s
b
y
name m
a
tching
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
es
s
re
m
ov
e
d commrec->nth
r
ead
s
from FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hes
s
gmx
c
heck n
o
w us
i
n
g
the diagonal fo
r
relat
i
ve tolerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k He
s
s
f
ixed g_e
n
ergy manu
a
l formattin
g
issues
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
grompp aut
o
matic ns
t
calcenergy setting
n
ow
take
s
s
m
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk H
e
ss
add
e
d full precision option
to
g_traj a
n
d reformatted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
fixe
d
PME com
m
un
i
cation range when
first DD di
m
is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
H
ess
ma
d
e vrescale and Bere
n
d
s
en tcouple work
w
ith
V
V
,
a
lthough
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk
H
ess
c
o
rrected LJ
o
n
H
of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk Hess
completed pa
r
tial re
n
ame of CYN to CYS fo
r
A
m
ber
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
e
s
s
correc
t
ed the Am
b
er aminoacids
.
r2b
fi
l
es
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
renam
e
d
pme_maxshift0/1 to p
m
e
_
m
a
xshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
B
e
r
k Hess
replaced the Ch
a
rmm v
s
ite par
a
m
eter
s
(which
w
e
re OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
erk He
s
s
c
o
rrected
a
vsit
e
parameter in the amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
correc
t
ed Cl atom
name in
a
mber ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber ff atomtypes change: co
r
rect
e
d mass
e
s
,
re
m
o
v
ed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
u
pda
t
e
o
f amber03 aminoacids
.
rtp
,
accid
e
n
t
a
lly left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected mistakes
i
n amber03 gbs
a
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
fixed ty
p
o in Make
f
ile
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k
He
s
s
moved ff_d
u
m
.
itp to the g
m
x a
n
d
gromos ff dir
e
ct
o
ries
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
c
orrected the amber
v
sit
e
parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk Hes
s
a
d
ded h
i
s to opls
r2b fil
e
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made the
ff file naming of amber
an
d
charmm c
o
nsis
t
ent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
c
o
rre
c
ted the a
m
ber water
model file
s
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PM
E
decomposition check
for inverse
DD ord
e
r
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
rename
d
a
m
ber LYP to LYS and
changed
n
a
mes for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
e
s
s
rem
o
ved HOH
f
rom amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
ed missing entri
e
s for amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k Hes
s
cle
a
ned
u
p Amber hdb's
and a
d
ded HO4
commit
|
commitdiff
|
tree
2010-07-26
B
erk H
e
ss
renamed atom ty
p
es from amber99_? etc
.
to the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
fixed
PME commu
n
i
c
at
i
o
n
ra
n
ge (no
s
i
l
e
n
t
err
o
rs)
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
removed building block
RT
f
rom the
list
s
in share/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
add
e
d
resi
d
u
e
and atom renaming fo
r
AMBE
R
d
n
a and rna
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
H
ess
added DNA
a
nd
RNA
to the pdb2gm
x
.
a
r
n format
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renam
e
d O to O2 in amber r
n
a
.
r
tp
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
added na
t
oms_f
o
rce_constr to t_for
c
erec
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
renamed O
t
o
O2 in amber
d
na
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
removed garb
a
ge from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
He
s
s
fixed (ra
r
e
)
incorre
c
t r
e
s
i
due nu
m
be
r
s when u
s
ing gmx_mt
o
p_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk H
e
s
s
a
dded op
e
nmm wr
a
pper R
F
p
a
r
a
m
eter checks
commit
|
commitdiff
|
tree
2010-07-19
B
e
rk H
e
ss
mino
r
update t
o
th
e
previos ap
p
ending fix
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
fix
e
d
mdrun append check when requested output file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hes
s
a
d
ded mdp par
a
m
e
ter
for FE d
H
tables
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
c
h
a
n
ged the d
e
fault maxim
u
m number of backups
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
rem
o
ved a lot of slow FFT gr
i
d sizes f
r
om calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
d
o
cu
m
ented
pull cosine
weightin
g
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
rename
d
mdrun -cptnum
t
o -cpnum
commit
|
commitdiff
|
tree
2010-06-28
B
e
r
k Hess
a
d
d
e
d md
r
un -c
p
tn
u
m
option to keep and
number che
c
k
points
commit
|
commitdiff
|
tree
2010-06-28
B
erk
Hess
r
ev
e
rt
e
d acc
i
dential change of tabangles in g
r
ompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
d
ded include up
d
ate
.
h t
o
c
oupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k Hess
a
d
ded back const to gmx_
s
ort compare params for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk
Hess
remo
v
ed obsole
t
e fftg
r
id code
a
nd disabled PPP
M
with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k
He
s
s
chan
g
ed pd
b
2gmx water mo
d
el
ato
m
c
ount detection
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk H
e
ss
i
mplemented nsteps=-1 f
o
r mdrun continuati
o
n and tpbco
n
v
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed sma
l
l
o
c
.
h and smalloc
.
c d
e
finition inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge branch 'master' of
g
it@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
B
er
k
Hess
remov
e
d s
t
atusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed gm
x
_eneconv compiler
w
a
r
nings
commit
|
commitdiff
|
tree
2010-06-23
Berk
Hess
fixed
en
e
conv -dt o
p
tion tempora
r
ily not writin
g
averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
corrected
e
dr format i
s
sue introduced
today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
add gmx_qsort routine, sin
c
e glibc
q
sort
i
s not threads
a
f
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
B
er
k
Hess
fixed typo
i
n
fata
l
_er
r
or call
commit
|
commitdiff
|
tree
2010-06-18
Ber
k
Hess
now mdrun does not wri
t
e
the trr file when it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
added
env var GMX_M
A
XBAC
K
UP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fix for the previous mdrun -rerun
c
ommit
commit
|
commitdiff
|
tree
2010-06-17
B
erk He
s
s
mdrun -
r
erun no
w
reads the re
r
un
t
raj only on th
e
mast
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
m
i
nor update for previous replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
B
e
r
k
Hess
fixe
d
mdrun -
r
erun giving N
a
N with dispcorr
commit
|
commitdiff
|
tree
2010-06-17
B
erk Hess
ad
d
ed wate
r
mode
l
select
i
on and list file to
pdb2gmx
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hess
made a separa
t
e tips3
p
.
i
tp file
f
or CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Merge
bra
n
ch 'master' of git
@
git
.
gromacs
.
o
r
g:grom
a
cs
commit
|
commitdiff
|
tree
next