[AMBER] NPT equilibration failed

From: Albert <mailmd2011.gmail.com>
Date: Tue, 18 Aug 2015 14:58:56 +0200


I am trying to equilibrate my system with heat & NVT followed by NPT.
The heat and NVT step finished without any errors. But the NPT failed
with messages:

   Unit 10 Error on OPEN: refc
application called MPI_Abort(MPI_COMM_WORLD, 1) - process

Here is the command I used:

mpirun -np 20 pmemd.MPI -O -i 01-mini.in -o mini.out -p sol.prmtop -c
sol.inpcrd -r mini.rst -ref sol.inpcrd
ambpdb -p sol.prmtop < mini.rst > mini.pdb
mpirun -np 2 pmemd.cuda.MPI -O -i 02-heat.in -o heat.out -p sol.prmtop
-c mini.rst -r heat.rst -x heat.mdcrd -ref mini.rst -inf heat.info
gzip -9 heat.mdcrd
ambpdb -p sol.prmtop < heat.rst > heat.pdb
mpirun -np 2 pmemd.cuda.MPI -O -i 03-density.in -o density.out -p
sol.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst
-inf nvt.info
gzip -9 density.mdcrd
ambpdb -p sol.prmtop < density.rst > density.pdb
mpirun -np 2 pmemd.cuda.MPI -O -i 04-npt.in -o equil.out -p sol.prmtop
-c density.rst -r equil.rst -x equil.mdcrd -inf npt.info
gzip -9 equil.mdcrd

This messages appeared in NPT step.

here is my input file:
   cut=10.0, ntb=2, ntp=1, taup=2.0,
   ntpr=1000, ntwx=1000,
   ntt=3, gamma_ln=2.0,
   ntr=1, restraintmask=':1-158',

thanks a lot

AMBER mailing list
Received on Tue Aug 18 2015 - 06:00:05 PDT
Custom Search