AMBER Archive (2005)

Subject: AMBER: REM difficulties

From: Peter Varnai (pv232_at_cam.ac.uk)
Date: Thu Nov 03 2005 - 12:15:01 CST

Hi,

I have compiled & tested sander and while trying to set up replica
exhange I noticed some strange behaviour:

* in "File Assignments" section INPCRD echoed always as RESTRT
* in my particular case using default i/o I have problems with mixed
  ext 000/001 (although in test it seemed to be OK):

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:

$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.

Thanks,
Peter
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