On Thu, Mar 19, 2015 at 2:02 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’ve just completed 50ps heating of my complex without any problems
>
> I’m now trying to do density equilibration using the following script:
>
> mpirun -np 8 sander.MPI -O -i density.in -o density.out -p
> cmplx_solv.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst
>
> The system aborts giving the following message
>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 614 RUNNING AT itvds-ws026.local
> = EXIT CODE: 1
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
>
> My density.in script is:
>
> density Agam(3n7h)-indole1-indole2-water
> &cntrl
> imin=0,irest=1,ntxo=2,
> nstlim=25000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=1.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0, ig=-1,
> ioutfm=1,
> temp0=300.0,
> ntr=1, restraintmask=':1-128',
> restraint_wt=2.0,
> /
>
> Any ideas of what’s likely to have caused this problem will be appreciated
>
All this error message says is that some problem happened, somewhere.
Look for an error message in the output file. The master thread (rank 0)
called abort, so it should have printed its problem to the end of the mdout
file.
Also, you set irest=1, but nothing with ntx. I suggest setting ntx=5 in
order to tell sander that velocities are present in the inpcrd file.
Last comment -- ntxo controls restart file format. That is almost
certainly not the problem.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 19 2015 - 11:30:04 PDT
