AMBER Archive (2008)

Subject: AMBER: REMD simulation error

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Wed Apr 02 2008 - 07:47:20 CDT

Hi Amber users,
I try to run a Replica Exchange MD simulation with Amber8, 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?
Thank you

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.
 /

------------------------------------------------------------------------

 # replica exchange log file
 # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
 # exchange 1
 1 1.03 298.22 -191.25 250.00 267.40
 2 0.97 289.24 -204.62 267.40 250.00
 # exchange 2
 1 0.97 292.24 -212.48 267.40 250.00
 2 1.03 260.87 -203.34 250.00 267.40
 # exchange 3
 1 1.03 210.47 -171.14 250.00 267.40
 2 0.97 267.19 -220.62 267.40 250.00
 # exchange 4
 1 0.97 250.31 -216.04 267.40 250.00
 2 1.03 242.25 -193.63 250.00 267.40
 # exchange 5
 1 -1.00 240.24 -190.41 250.00 250.00
 2 -1.00 268.46 -177.31 267.40 267.40

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