Hi Aneesh,
It is not an AMBER response of your question but I don't know why you want to keep the protein at the center of RM, since for me what you observe is normal for protein/peptide confined in RM. Indeed depending the charges at protein/peptide surface and the surfactant headgroup type, you will observe the same behavior. Furthermore, you can keep in mind that the RM water pool size (e.g. greater than protein size) will also favor the diffusion of the confined protein in RM interior.
Hope it helps
Stefane
------------------------------
Stéphane Abel, PhD
CEA Saclay DSV/IBITEC-S/SB2SM
91191 Saclay, FRANCE
website: http://www.st-abel.com
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________________________________
De: aneesh cna [mailto:aneeshcna.gmail.com]
Date: lun. 30/08/2010 10:24
À: AMBER Mailing List
Objet : [AMBER] Regarding protein diffusion
Dear Amber users,
I am working with the simulation of protein in reverse micelle.
During the course of simulation protein is found to be diffuse towards the
wall of the reverse micelle and making interaction with surfactants. I want
to keep the protein at the center of the reverse micelle. Is there any way
to do this in Amber?. I am using Amber 9.0.
Thanks in advance
Sincerely
Aneesh
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Received on Mon Aug 30 2010 - 07:30:03 PDT
