From: David Tanner (guacamoleo_at_gmail.com)
Date: Sun Apr 17 2011 - 06:39:19 CDT
I don't have an answer, but here is a paper which partially addresses
that question.
http://crystal.med.upenn.edu/sharp-lab-pdfs/prabhu_zapdna_Jcompchem_29.pdf
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
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On Apr 17, 2011, at 12:30 AM, marawan hussain wrote:
HI David,
i want to know how can i neutralize by adding ions prior to
submission to MD run using the implicit solvation model in NAMD 2.8.
Do i need to solvate first then neutralize by ions addition then
remove the water molecules and submit to the MD run using the implicit
solvent model or this implicit solvation model can handle the
unneutralized (charged)protein.
Thanks
Marawan
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