Re: Changing the atomtype of a particle on the fly

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Sun Oct 04 2009 - 18:59:00 CDT

If my server administrator read this I will have to delete all my
scripts..jeje.
I usually do that to run multiple steps simulations without wait a long time
on
the queue.

Best
DAV

On Fri, Oct 2, 2009 at 3:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, 2009-10-02 at 11:50 -0700, BIN ZHANG wrote:
> >
> >
> > So you mean if I include the following loop in the PBS script:
> > for (( i = 0; i<=100; i++ ))
> > do
> > namd2 namd_input_$i
> > done
> > , then the jobs will simply run one by one?
> >
>
> yes. of course. why not?
>
> pbs has absolutely no idea about what you are doing.
> it just reserves a number of nodes or rather slots
> and executes the script you give it on the head node/slot
> and waits until the script is done to release the
> reserved resources. there is no magic there.
>
> if you reserve multiple nodes to be used with MPI,
> you can even submit different parallel jobs on subsets
> of the reserved block of nodes/slots by backgrounding
> them and then put just a "wait" into the script to
> wait for all of them to finish so that the script
> only terminates if all of them are done.
>
> cheers,
> axel.
>
>
>
> >
> > That will be great!
> >
> >
> > Thanks,
> > Bin
> >
> >
> >
> >
> > On Oct 2, 2009, at 11:30 AM, Axel Kohlmeyer wrote:
> >
> > > On Fri, 2009-10-02 at 11:23 -0700, BIN ZHANG wrote:
> > > > Dear Axel:
> > > >
> > > > Thanks for your reply.
> > > >
> > > > You will be absolutely right in an ideal world. However, I'm
> > > > planning
> > > > on running a CG simulation approaching 1 micro S timescale. Also,
> > > > I
> > > > will be running my jobs on a queuing system, so too frequent
> > > > restarting will increase the waiting time on the queue.
> > >
> > > ...and in a real world you would just put multiple namd
> > > executions into a single script file that you submit
> > > to the batch system and then you are fine again.
> > >
> > > other than that, the NAMD source code is available
> > > for download, so feel free to implement this hack yourself.
> > >
> > > cheers,
> > > axel.
> > >
> > >
> > > > Bin
> > > >
> > > > On Oct 2, 2009, at 11:09 AM, Axel Kohlmeyer wrote:
> > > >
> > > > > On Thu, 2009-10-01 at 23:15 -0700, BIN ZHANG wrote:
> > > > > > Dear All:
> > > > >
> > > > > dear bin,
> > > > >
> > > > > > Is it possible to change the atom type of a particle on the
> > > > > > fly
> > > > > > without stopping the simulation? Say, after one ns simulation,
> > > > > > I want
> > > > > > to change the parameter for a particular particle (alternating
> > > > > > the
> > > > > > parameter for LJ balls).
> > > > > >
> > > > > > Any suggestions is appreciated.
> > > > >
> > > > > if you run for one nanosecond, the time for startup
> > > > > should be negligible compared to runtime. so why bother?
> > > > >
> > > > > just prepare the necessary topology/parameter files
> > > > > ahead of time and you should be fine and run them
> > > > > one after the other.
> > > > >
> > > > > cheers,
> > > > > axel.
> > > > > >
> > > > > > Thanks,
> > > > > > Bin
> > > > > >
> > > > > >
> > > > > --
> > > > > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> > > > > Institute for Computational Molecular Science
> > > > > College of Science and Technology
> > > > > Temple University, Philadelphia PA, USA.
> > > > >
> > > >
> > > --
> > > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> > > Institute for Computational Molecular Science
> > > College of Science and Technology
> > > Temple University, Philadelphia PA, USA.
> > >
> > >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>

-- 
saludos desde el fin del mundo

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