AMBER Archive (2008)

Subject: AMBER: REMD simulation error

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Fri Mar 28 2008 - 09:01:20 CDT

Hi everyone,
I try to run a Replica Exchange MD simulation, but after a few cycles,
the program crashes with the error message:

  Unit 6 Error on OPEN: md.out.000

  Unit 6 Error on OPEN: md.out.001
MPI: On host soleil1, Program /usr/local/amber8/exe/sander.REM, Rank 1,
Process 3058 called MPI_Abort(<communicator>, 1)

I've launched the simulation with the command:
mpirun -np 2 sander.REM -O -ng 2 -rem 1 -remlog rem.log -i md.in -o
md.out -p peptide.parm -c md.crd -r md.rst -x md.mdcrd
and the ouput files look fine.
I've sent the remlog and the input files in attachment.
Does anyone have an idea of what is happening?
Thanks

Guillaume

input for Replica 2
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=2000, numexchg=50000, dt=0.001, temp0 = 267.4,
  ntc=1, ntf=1,
  ntt=3, gamma_ln = 20,
  ntpr=50, ntwx=50,
  ntb=0,
  cut=12.
 /

input for Replica 1
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=2000, numexchg=50000, dt=0.001, temp0 = 250,
  ntc=1, ntf=1,
  ntt=3, gamma_ln = 20,
  ntpr=50, ntwx=50,
  ntb=0,
  cut=12.
 /


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu