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renamed O to O2 in amber dna.rtp
2010-07-26
Be
r
k Hess
renamed O to O2 in
a
mber dn
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
ess
remov
e
d ga
r
b
a
ge from c
h
eckpoi
n
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
B
erk H
e
ss
fixed (rare)
i
nc
o
r
r
ect
residue number
s
wh
e
n
u
si
n
g gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
e
ss
add
e
d openmm wrapper RF p
a
rameter checks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
minor update to
t
h
e previos appen
d
i
n
g fi
x
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
es
s
fixed mdru
n
a
p
pe
n
d check when requested
output
f
ile
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk
Hes
s
added m
d
p para
m
e
ter for
FE dH table
s
commit
|
commitdiff
|
tree
2010-07-05
B
e
rk Hess
chan
g
ed the defa
u
lt maximum number of backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
B
erk He
s
s
rem
o
v
ed a lot of slo
w
FFT grid sizes from calc
_
grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
d
o
cume
n
ted pull cosine weightin
g
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
re
n
amed mdrun -cptnum to -cpnum
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
add
e
d
mdrun
-
cptnum
o
ption to ke
e
p
an
d
number checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted
accidentia
l
chang
e
of tabangles in gr
o
mpp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added inclu
d
e update
.
h
to couplin
g
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
dded b
a
ck cons
t
to gm
x
_sort compare params for qso
r
t
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
r
e
mov
e
d obsolete ff
t
grid code
and disabled
PPPM with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
cha
n
g
ed pdb2gmx water model atom count detection
commit
|
commitdiff
|
tree
2010-06-24
Berk He
s
s
impl
e
mented
nsteps=-1 f
o
r mdrun cont
i
nu
a
t
i
on and tpbco
n
v
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
f
ixed smalloc
.
h
and small
o
c
.
c definition
inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k Hess
Merge br
a
nch '
m
aster'
of git@
g
it
.
gr
o
ma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Ber
k
H
e
ss
remov
e
d
statusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
f
ixed gmx_eneconv compil
e
r warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fix
e
d
e
neconv -dt opti
o
n tempora
r
i
ly
n
o
t
writing averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
co
r
rec
t
ed edr format issue i
n
troduced
t
oday
commit
|
commitdiff
|
tree
2010-06-21
B
e
rk Hess
add gmx_qsort ro
u
tine, since glibc qso
r
t is n
o
t
t
h
readsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk
He
s
s
fixed
t
y
po in fatal_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now md
r
u
n
do
e
s
no
t
w
r
ite the trr file when
it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
B
erk Hess
added env var
G
MX_M
A
X
BACKU
P
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
f
i
x for
t
h
e prev
i
ous mdrun -re
r
un commit
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
m
d
run -
r
erun now reads the r
e
r
u
n
traj only on the m
a
ster
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
minor
u
p
date for prev
i
o
us replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
fixed mdrun -rerun giving NaN
w
ith dispcorr
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk
Hess
added water model
sel
e
ction
a
n
d list file to pdb2
g
mx
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
made a separate tips3p
.
it
p
file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Merge b
r
anc
h
'master
'
o
f
git@git
.
grom
a
cs
.
o
rg:gr
o
macs
commit
|
commitdiff
|
tree
2010-06-16
B
erk Hess
ad
d
ed spce
to charmm27
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixe
d
MPI cra
s
h when nat_ho
m
e=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
restored the old
or
d
e
r
of t
h
e
m
drun opt
i
on and removed
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
r
eplace
d
m
ore gmx
_
fatal by collective ca
l
ls in DD
commit
|
commitdiff
|
tree
2010-06-16
Be
r
k H
e
s
s
fixed atom nam
i
ng i
n
enca
d
c-term
i
ni
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
with
n
s
teps=-1 mdrun now
prin
t
s ns/
d
ay e
s
timate
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
Hess
added
nste
p
s=-1 o
p
t
i
on to m
d
p_opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
Berk H
e
ss
all energy minimizers
now
d
o 0 steps with nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fixed i
n
correct pdb2
g
mx CYS2 to CYS re
n
am
i
n
g which
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
B
e
r
k
H
ess
allvs
a
ll loops n
o
w trigger particle d
e
composition
commit
|
commitdiff
|
tree
2010-06-15
Berk H
e
s
s
fatal_error
i
n th
e
DD ini
t
ializa
t
ion now ca
l
l
s MPI_Finalize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk
Hess
added -cwd
option to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
Berk Hess
fixed mdrun counter
r
e
s
ett
i
ng issues
commit
|
commitdiff
|
tree
2010-06-11
Ber
k
H
es
s
opti
m
ized the
n
umber
o
f threads
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
made DD work pro
p
erly with all non-periodic system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk
H
e
s
s
added more explanatio
n
to idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk H
e
ss
f
i
xed uniniti
a
lized variable
i
n do_m
d
commit
|
commitdiff
|
tree
2010-06-10
Be
r
k Hess
fixed particl
e
decom
p
o
sition load print
commit
|
commitdiff
|
tree
2010-06-04
B
e
rk Hess
fixed pdb2g
m
x messing up coordinates when
deleting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
B
e
rk
H
ess
ad
d
ed no
t
es on md
p
dis
r
e
p
a
rameters
commit
|
commitdiff
|
tree
2010-06-03
B
erk Hess
distance restra
i
nt ensemble averagin
g
i
s
no longer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk He
s
s
fixed
bug in enu
m
parsing e
r
r
o
r messag
e
commit
|
commitdiff
|
tree
2010-06-03
B
erk
H
ess
added VV param
e
ters to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-02
Berk Hes
s
fixed
more
G
romos atom
t
y
pe
n
ame cases
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
clean
e
r fix
for
atom
t
ype
c
ase issue with GB par
a
meter
s
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixe
d
a
t
om type cas
e
issue with GB parameters
commit
|
commitdiff
|
tree
2010-06-01
Berk Hes
s
fixed two GB bugs
commit
|
commitdiff
|
tree
2010-05-19
Be
r
k Hess
fixed mdrun un
w
antingly modifying nst
e
n
e
rgy and nstlog
commit
|
commitdiff
|
tree
2010-05-18
B
e
r
k He
s
s
i
m
pl
e
ment S
S
E exp calc
u
lation
f
or
s
olve_pm
e
commit
|
commitdiff
|
tree
2010-05-17
B
e
rk
H
es
s
f
i
xed some ge
n
born incl
u
de
f
ile
de
t
ails
commit
|
commitdiff
|
tree
2010-05-17
Berk Hess
reordered pme_solve_yzx arguments
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
minor pme
_
sol
v
e viria
l
optimization
commit
|
commitdiff
|
tree
2010-05-14
Berk He
s
s
fixed se
g
v with md
r
un -npm
e
1
commit
|
commitdiff
|
tree
2010-05-12
Ber
k
Hes
s
fixed case of atom
t
ypes in the Gr
o
mos force fields
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
corrected
p
db
2
gmx force
f
ield comment
s
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
made atom
t
ypes case se
n
sitive
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
fixe
d
bug in pdb2gmx hdb initialization
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
added
proper DNA and RNA residue r
e
cognition
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
added prop
e
r DNA and RNA
r
e
sidue
r
ecognition
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
fixed incorrect pdb2gmx residue name mat
c
hing with
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
fixe
d
bug with pdb2gmx and multiple rtp files
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
add
e
d check f
o
r sys/time
.
h e
x
istence
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
updated and fine-tun
e
d the coeffici
e
n
t
s
f
or the PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
Ber
k
Hess
removed i
n
clu
d
e of compl
e
x
.
h i
n
f
f
t5d
.
h
commit
|
commitdiff
|
tree
2010-05-10
Berk Hes
s
fixed
u
nderall
o
c
a
ti
o
n
in gmx_fft_init_many_1d_real
commit
|
commitdiff
|
tree
2010-05-10
B
erk Hess
fixed
name in gromos43a
1
.
ff Makef
i
le
.
am
commit
|
commitdiff
|
tree
2010-05-10
Berk He
s
s
moved al
c
o
h
ol files f
r
om top
to the fo
r
ce field
subdirectories
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
mov
e
d alcohol files from top to the
f
orce fi
e
ld subdirect
o
ries
commit
|
commitdiff
|
tree
2010-05-10
Berk
Hess
completion of the pdb2g
m
x residue
renami
n
g
change
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
changed internal Gromacs naming of cys, hi
s
and l
y
s
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
added a column fo
r
single residue chain to r
2
b
file
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
fixed
segv i
n
grompp when gm
x
cpp reports an error
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
made gro
m
pp cha
r
g
e
warning
le
s
s
sensitive t
o
rounding
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
Berk
Hess
m
a
d
e
PME energy and vi
r
ial calculation optional
commit
|
commitdiff
|
tree
2010-05-07
B
erk
H
ess
Merge com
m
it
'
origin/2d
p
me
'
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
remove
d
solve_xyz
commit
|
commitdiff
|
tree
2010-05-07
B
e
r
k
H
e
ss
nst
e
n
e
rgy is now -1 by default, meanin
g
nstlist
commit
|
commitdiff
|
tree
2010-05-06
Berk
Hess
fixed some d
e
tails for
ns
t
calcene
r
g
y
>1
commit
|
commitdiff
|
tree
2010-05-04
Berk Hess
fixed compiler
war
n
ing
commit
|
commitdiff
|
tree
2010-05-03
Berk Hess
remov
e
d incorrect
PME grid factor ch
e
ck
commit
|
commitdiff
|
tree
2010-05-03
Berk Hess
added some explanati
o
n
commit
|
commitdiff
|
tree
2010-04-30
Berk H
e
ss
Merge
commit 'origin/master' into 2dpme
commit
|
commitdiff
|
tree
2010-04-30
Berk He
s
s
co
r
rected pm
e
gather flop c
o
u
n
t
from 12 to 6
commit
|
commitdiff
|
tree
2010-04-30
B
e
r
k
Hess
fixe
d
re
s
t
cycle c
o
u
nt in seri
a
l
commit
|
commitdiff
|
tree
2010-04-30
B
e
rk He
s
s
f
i
xed mu
l
tiple print
of run termination message
commit
|
commitdiff
|
tree
next