hello,
sander.MPI (Amber9) seems to be writing part junk (binary?) to output. i am
using a regular groupfile, the &cntrl section like this ...
100ps nve heating
&cntrl
imin=0,
ntr=0,
nstlim=50000,
nscm=1000,
ntx=1,
irest=0,
ntb=1,
ntp=0,
ntt=3,
gamma_ln=1.0,
tempi=0.0,
temp0=300.0,
dt=0.002,
nrespa=1,
ntc=2,
ntf=2,
noshakemask=":fmn",
ntwr=1000,
ntwx=1000,
ntwe=1000,
ntpr=1000,
cut=9.0,
icfe=1,
clambda=0.0000,
klambda=1,
/
the principle difference between 'normal' and 'problem' output files is in the
`Noshake mask` section, where normally ...
.. snip ..
Noshake mask :fmn; matches 50 atoms
Removing shake constraints from C5_ fmn 139 -- H17 fmn 139
Removing shake constraints from C5_ fmn 139 -- H18 fmn 139
.. snip ..
i am instead seeing the following,
.. snip ..
Noshake mask :fmn; matches 50 atoms
Removing shake constraints from ^.^.^.^.^.^.^.^.^.^.^.^.^. --
^.^.^.^.^.^.^.^.^.^.^.^.^.
Removing shake constraints from ^.^.^.^.^.^.^.^.^.^.^.^.^. --
^.^.^.^.^.^.^.^.^.^.^.^.^.
.. snip ...
a DV/DL 'Averages' section is written every 1000 steps but all values in this
section are zero for this latter simulation. when i query the latter file type
(using the linux tool `file`), it reports "data". for the former, with
apparantly identical input (setup procedure, although different prmtop and
inpcrd files), `file` returns "ASCII English text".
I wonder anyone has come across this before? any pointers gratefully recieved,
best wishes, Ben.
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Received on Sun Jun 03 2007 - 06:07:15 PDT
