From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Fri Oct 02 2009 - 13:50:21 CDT
So you mean if I include the following loop in the PBS script:
for (( i = 0; i<=100; i++ ))
, then the jobs will simply run one by one?
That will be great!
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.
>> 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
>>>> 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.
>>> 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.
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