AMBER Archive (2009)

Subject: Re: Re: [AMBER] MD simulation with a partially flexible system

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Tue Feb 17 2009 - 20:19:47 CST

Hi Carlos,

    Thanks for the reply. What I want to do is trying to reduce the computational cost by focusing only a small part of the whole system. Since we only concerns the dynamical change of a subdomain, it can be reasonable to allow only the subdomain and its neighbouring atoms to move while keeping the rest atoms rigid during the simulation, which I thought the computational cost would reduce greatly compared to keeping the whole system flexible.

Thanks very much for the time.

---
Jeffrey


>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_at_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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