[gmx-users] Sum of the two largest charge groups radii is larger than rlist!!!

[Justin Lemkul]

On 10/18/12 5:26 AM, Arman M. Soufiani wrote:
> Dear Friends,
>
> I am simulating a protein-polymer interactive system.
> I faced two problems.
> First, when I added the ions to my solvated system, the polymer structure
> shifted a little bit out of the PBC box. I really have no idea why this
> happened!

There is no "outside" of a periodic system.  You haven't said what your box 
shape is, but if, for example, you use a dodecahedral box, in its triclinic 
form, even a centered molecule may seem to stick "outside" the box.

> I ignored this issue and proceed to EM, which I don't know if the problem
> mentioned above will make me into trouble or not.
> Anyhow, I tried to compose the .tpr file. However, the following error
> appeared:
>
> *The sum of the two largest charge group radii (6.907749) is larger than
> rlist (1.000000)*
>
> I would be thankful if anyone can help me with these issues.
>

The error indicates you have very large charge groups (too many atoms), which 
can negatively impact neighbor searching and calculations of nonbonded 
interactions, leading to artifacts.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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