can you be more clear about how you want to reduce the computational
expense? are you following an example from the literature, or just
trying it out to see if it can be done?
you could use the belly option, but the details of how well this works
depend on whether your simulation is periodic, or if you use GB
solvent, etc. you won't always get much improvement in speed, and also
the belly option can have issues with PBC, you can find out more about
that in the archives.
On Tue, Feb 17, 2009 at 9:38 AM, Jeffrey <jeffry20072008.yahoo.cn> wrote:
> Dear amber users,
>
> I'd like to perform a microsecond-scale MD simulation to see the change of a subdomain with time. So it is necessary to reduce the computational expense by keeping only the subdomain and its surrounding atoms to move while keeping the rest of the system as rigid body during the course of simulation. I checked the amber mannual and didn't find a good choice.
> Does anyone know whether this job can be done in AMBER package?
>
> Thanks very much.
>
> ------
> Jeffrey
>
>
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Received on Wed Feb 18 2009 - 01:19:31 PST
