Thank you very much for your inputs Professor Case and Jason! I seem to have
identified the problem. It had someting to do with the rst file. But, I
don't know the solution to it.
I performed 2 sets of minimization and then went on to perform the MD.
1) 1000 steps of steepest descent
steepest
&cntrl
imin=1, ntmin=2, maxcyc=1000,
cut=10.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
/
2) This is followed by 1000 steps of Polak-Ribiere conjugte gradient
polak
&cntrl
imin=1, ntmin=3,
irest=0, ntx=1,
maxcyc=1000,
cut=10.0,ntb=0,
ntc=2,ntf=2,
ntpr=100,
drms = 0.0119,
/
&lmod
xmin_method = prcg,
/
Now when I perform subsequent MD simulations (input file shown below) with
the rst generated from the first step they work fine. But, when I try them
with the rst generated from the PRCG (second) step no output files are
generated. I suspect something is wrong with the second input. So where
exactly is the error in the input file?
Here is the input for subsequent simulations using rst's generated from 1
& 2
MD
&cntrl
imin=0, irest=0, ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntp=1,taup=2.0,
/*
*
Thanks,
Jagdeesh
On Sun, Jun 20, 2010 at 9:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Jun 20, 2010 at 11:32 AM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Sun, Jun 20, 2010, Jagdeesh C wrote:
> > >
> > > I am trying to perform a few ps heating. I have the prmtop, heat.in,
> and
> > > restart file which seem to look fine. However the heating simulation
> > doesn't
> > > work and the final files are not generated (no output). I have been
> > trying
> > > to rectify it but I seem to be going wrong somewhere. Can someone
> please
> > > help me and let me where I might be going wrong?
> > >
> > > Many thanks,
> > > Jagdeesh
> > >
> > >
> > > ./sander.MPI -O -i heat_143d.in -o heat_143d.out -p 143d_sol.prmtop -c
> > > min_143d.rst -r heat_143d.rst -x heat_143d.mdcrd -ref min_143d.rst
> >
>
> Professor Case is right -- mpirun or mpiexec or something of the like (it
> differs based on the system) is typically needed to run sander.MPI, though
> this usage usually starts a single sander.MPI thread on my machines (i.e.
> it
> will be more or less the same as running serial sander). This may not be
> true for all MPIs, though, I don't know.
>
> However, why are you using "./sander.MPI"? Is sander.MPI in the directory
> you're trying to run from? That seems like an unusual choice, since
> sander.MPI is usually in $AMBERHOME/bin, and I'd suggest that running jobs
> in that directory should be avoided (though it won't cause any errors).
> (Unless of course you're creating a link in your current directory to
> $AMBERHOME/bin/sander.MPI) Do you get any complaints from the command line,
> such as not being able to find sander.MPI?
>
> All the best,
> Jason
>
>
> > You need to use mpirun with sander.MPI: you can't just call it directly.
> > I'm not sure if this is the reason you are getting "no output", but it's
> > certainly worth checking.
> >
> > General advice: if you are having problems, run the serial version of the
> > program, use just a few steps (say 50, not 50,000), set ntpr=1, and very
> > carefully study your output files. Later on you can increase the number
> of
> > steps, etc.
> >
> > ...good luck...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
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>
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Received on Tue Jun 22 2010 - 20:30:03 PDT
