Hi,
There is a pretty clear error message in your output file:
> | peek_ewald_inpcrd: Box info not found in inpcrd
You have ntb > 0 in your input which implies periodic boundary
conditions but your input coordinates have no unit cell information.
You either need to add box information or change ntb to 0 (and other
parameters as appropriate).
-Dan
On Wed, Jun 21, 2017 at 5:23 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com> wrote:
> Dear Amber list
> I am trying to do MD simulation on my complex. I did minimization step, heat and density using the input files:
> min.inminimise complex &cntrl imin=1,maxcyc=1000,ncyc=500, cut=10.0,ntb=0,igb=5, /
> heat.inheat complex &cntrl imin=0,irest=0,ntx=1, nstlim=25000,dt=0.002, ntc=2,ntf=2, cut=10.0, ntb=0, ntpr=500, ntwx=500, ntt=3, gamma_ln=2.0, tempi=0.0, temp0=300.0, ntr=1, restraintmask=':1-499', restraint_wt=2.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=25000, value1=0.1, value2=300.0, / &wt TYPE='END' /
> density.inheat ron-msp &cntrl imin=0,irest=1,ntx=5, nstlim=25000,dt=0.002, ntc=2,ntf=2, cut=10.0, ntb=0, ntp=0, taup=1.0, ntpr=500, ntwx=500, ntt=3, gamma_ln=2.0, temp0=300.0, ntr=1, restraintmask=':1-499', restraint_wt=2.0, /
> But when I perform equilibration step I got the following error:
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.You may or may not see output from other processes, depending onexactly when Open MPI kills them.
> equil.in
> heat complex &cntrl imin=0,irest=1,ntx=5, nstlim=250000,dt=0.002, ntc=2,ntf=2, cut=12.0, ntb=0, ntp=1, taup=2.0, ntpr=1000, ntwx=1000, ntt=3, gamma_ln=2.0, temp0=300.0, ig=-1, /
>
> The equil.out file is attached. Any help would be highly appreciated.
> ThanksMaryam
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>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jun 21 2017 - 06:00:10 PDT
