Peter,
we're doing some changes and cleanup of these options for amber9.
>* in "File Assignments" section INPCRD echoed always as RESTRT
>
>
the names are switched so that the input file is always the restart from
the previous exchange
>* in my particular case using default i/o I have problems with mixed
> ext 000/001 (although in test it seemed to be OK):
>
>
>
are you writing replica outputs or temperature-based outputs?
>File Assignments:
>| MDIN: run.in.001
>| MDOUT: run2.out.000
>|INPCRD: run2.rst.001
>| PARM: prmtop
>|RESTRT: run2.rst.001
>| REFC: refc
>| MDVEL: mdvel
>| MDEN: run2.ene.001
>| MDCRD: run2.trj.000
>
>* I tried to enforce filenames with groupfile but for some reason it
> seems to be rem = 0 and no replica exchange takes place:
>
>
>
I don't use groupfiles myself so I'd have to look into this, or someone
else may comment.
>$mpirun -np 2 $sander -rem 1 -ng 2 -groupfile groupfile
>
>where groupfile (on four lines):
>
># replica 1
>-O -i run.in.000 -o run2.out.000 -p prmtop -c run.rst.000 -r run2.rst.000 -x run2.trj.000 -e run2.ene.000
># replica 2
>-O -i run.in.001 -o run2.out.001 -p prmtop -c run.rst.001 -r run2.rst.001 -x run2.trj.001 -e run2.ene.001
>
>* if the temp0 is identical in the input files I can still run the
>simulation (this is my goal as I want to use average NMR restraints)
>but no output file appears for the individual replicas.
>
>
>
the code cannot handle the same temp0, this exchange is temperature-based
so you end up dividing by zero if they match. Amber9 will check the
inputs for this.
maybe if you explain more about what you're trying to do I could make
specific
suggestions- for now Amber only does replicas at different bath
temperatures.
carlos
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Received on Thu Nov 03 2005 - 18:53:00 PST
