[gmx-users] Sum of the two largest charge groups radii is larger than rlist!!!
Arman Mahboubi Soufiani
armansoufiani at gmail.com
Thu Oct 18 12:37:53 CEST 2012
Many thanks Justin for your thorough explanation.
On Thu, Oct 18, 2012 at 12:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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
> 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
>> *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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