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

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 12:30:43 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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