Hello:
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:
#minimization
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
#heating
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
#NVT
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
#NPT
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:
NPT
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1, restraintmask=':1-158',
restraint_wt=2.0,
/
thanks a lot
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Received on Tue Aug 18 2015 - 06:00:05 PDT
