Re: Changing the atomtype of a particle on the fly

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 02 2009 - 13:30:57 CDT

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:32 CST