On Sun, Jan 12, 2014 at 12:26 AM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> Dear All
>
> I restart the MD simulation for the second time, but there is a error about
> restart file. the first, second input and md3.out files are in the below.
> I am sorry to copy the out file so I forward the email again.
>
> your sincerely
> s. nasiri
>
> =========================================================
> equilibration for box
> &cntrl
> imin=0, ntpr=1000, ntwx=1000,
> ntx=5, irest=1,
> tempi=298., temp0=298., ntt=3, cut=12,
> gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=25000000,
> ntwr=1000, dt=.001, ig=-1,
> &end
> ==========================================================
> first
> /home/s.nasiri/openmpi/bin/mpirun -np 48 -machinefile $PBS_NODEFILE sander
> -O -i mdin.in -o md1.out -p ionicbox.prmtop -c min.x -r md1.x -x md1.nc -e
> md1.dat
>
> second
> /home/s.nasiri/openmpi/bin/mpirun -np 48 -machinefile $PBS_NODEFILE sander
> -O -i mdin.in -o md2.out -p ionicbox.prmtop -c md1.x -r md2.x -x md2.nc -e
> md2.dat
>
> third
> /home/s.nasiri/openmpi/bin/mpirun -np 48 -machinefile $PBS_NODEFILE sander
> -O -i mdin.in -o md3.out -p ionicbox.prmtop -c md2.x -r md3.x -x md3.nc -e
> md3.dat
> =========================================================================
> cat md3.out
>
> -------------------------------------------------------
> Amber 12 SANDER 2012
> -------------------------------------------------------
>
> | Run on 01/12/2014 at 08:15:03
> [-O]verwriting output
>
> File Assignments:
> | MDIN: mdin.in
>
> | MDOUT:
> md3.out
> |INPCRD:
> md2.x
> | PARM:
> ionicbox.prmtop
> |RESTRT:
> md3.x
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> md3.dat
> | MDCRD: md3.nc
>
> |MDINFO:
> mdinfo
> | MTMD:
> mtmd
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
> |INPTRA:
> inptraj
> |
>
> Here is the input file:
>
> equilibration for
> box
> &cntrl
>
> imin=0, ntpr=1000,
> ntwx=1000,
> ntx=5,
> irest=1,
> tempi=298., temp0=298., ntt=3,
> cut=12,
> gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
> nstlim=25000000,
> ntwr=1000, dt=.001,
> ig=-1,
> &end
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> |
> Flags:
>
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> peek_ewald_inpcrd: SHOULD NOT BE HERE
>
This indicates that there is likely a problem with your restart file. What
happens when you try to visualize your md2.x restart file with VMD (or
some other program)? Does it display a reasonable structure? Do you see
any * characters in your restart file? (If so, you should use "iwrap=1" or
use "ntxo=2" in your input file to turn on wrapping and NetCDF restart
files, respectively).
If you can't figure out what went wrong, you can attach your md2.x file so
we can take a look (although it would be useful if you can inspect the file
yourself and compare it to the format described on
http://ambermd.org/formats.html to see if you can figure out the issue
yourself).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jan 11 2014 - 22:00:02 PST
