AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: Eddie Men (pckboy_at_gmail.com)
Date: Wed Dec 19 2007 - 15:40:24 CST

Does a simulation need to be charge equilibrated?

I am running some MD simulations with my total charge equals -4

edu
Bill Ross wrote:
>> On Wed, Dec 19, 2007, Pablo Englebienne wrote:
>>
>>
>>>> Yes, water was added after adding the ions as recommended in the amber
>>>> manual. The number of counter ions added corresponds to the charge of
>>>> the protein so it is neutralized, ofcourse. :-)
>>>>
>>>> charge mol
>>>> addIons mol Na+ 250
>>>> solvateBox mol TIP3PBOX 8
>>>>
>> Of course I don't know why a 7500 residue system is "really unstable", but you
>> should look (visually) at the distributions of ions you get. Also, it is
>> certainly worth solvating *before* the addIons step: that is what I would
>> recommend, and I don't know where in the manual it states otherwise(?).
>>
>
> Doing addIons this way reduces gaps in the solvent.
>
> Also, how did you equilibrate? (Not sure if this was mentioned before.)
>
> Bill
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