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
--
========================================
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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