Re: Changing the atomtype of a particle on the fly

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++ ))
do
      namd2 namd_input_$i
done

, then the jobs will simply run one by one?

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.
>

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