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
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Received on Sat Jan 11 2014 - 21:30:03 PST
