you have a restraintmask but no -ref flag in your job script
you had that in your previous runs, but not in the NPT section
Also PLEASE PLEASE PLEASE add ig=-1 to your langevin thermostat inputs!
Oterwise you can see unphysical behaviors. Please look at the manual for
the origin of this requirement.
adrian
On 8/18/15 8:58 AM, Albert wrote:
> 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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--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Aug 18 2015 - 06:30:03 PDT
