AMBER Archive (2007)

Subject: AMBER: junk in `Noshake mask` output section

From: Ben Sattelle (ben.sattelle_at_postgrad.manchester.ac.uk)
Date: Wed May 30 2007 - 16:23:49 CDT

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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