AMBER Archive (2009)

Subject: Re: [AMBER] about MD simulation

From: Carlos Simmerling (
Date: Wed Mar 11 2009 - 05:56:43 CDT

I strongly recommend that you read articles in the literature that are
similar to what you are trying to do, and see what they did. papers tell you
details like # waters in the methods sections. since you haven't told us
anything about your system, we don't know if it's reasonable (but 20,000
could easily be ok). I can't stress enough, though, how important it is to
read the literature as a source of examples- not just the manual. then you
will see whether your goals are practical and readily obtained, or extremely
difficult, or somewhere in between. otherwise you will have no idea what to

On Wed, Mar 11, 2009 at 5:19 AM, ໪ <> wrote:

> Hi Prof. ,
> When I add water to the complex using "solvateoct unit TIP3PBOX 8.0" , it
> adds nearly twenty thousands water molecules. Is it abnormal?
> And somebody suggest me use solvateshell to do that, my queation is that :
> is it enough to add solvent only using solvateshell? Thanks!
> All the best!
> Qinghua Liao
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> ؿ㷢ؿȫߣ
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