Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors

From: Zhonghua Xia <zhonghua.xia.helmholtz-muenchen.de>
Date: Fri, 9 Nov 2018 14:27:07 +0100

Dear all,

Appreciate for all your help! Many thanks!

My plan is to obtain more probable conformations of my protein.

I’m going to try all your recommendatory methods, like H-REMD, aMD and GAMD.

What’s more, I’m also trying Hybrid-REMD which is introduced in Amber manual, applying a hybrid solvent system referring to both explicit and implicit model.

Let’s see what I would gain.

Best,
Zhonghua

> On 7. Nov 2018, at 23:40, Wesley Michael Botello-Smith <wmsmith.uci.edu> wrote:
>
> You might consider AMD (accelerated MD) or GAMD (gaussian accelerated MD).
> For a system of this size, those should be very feasible.
>
> On Wed, Nov 7, 2018 at 7:24 AM Zhonghua Xia <
> zhonghua.xia.helmholtz-muenchen.de> wrote:
>
>> Dear all,
>>
>> I want to do T-REMD on my protein (88 AA, 1438 atoms) with TIP3P water box
>> (5938 water molecules), as well as a counterion Cl-. I learn from the
>> tutorial that the number of replicas should be equal to the square root of
>> the total number of atoms. In my case, about 120 replicas…
>>
>> Any help appreciated! My purpose is certainly to enhance sampling.
>>
>> Kind regards,
>> Zhonghua_______________________________________________
>> AMBER mailing list
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>>
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Received on Fri Nov 09 2018 - 05:30:03 PST
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