Chih-Ying Lin wrote:
Hi
How to set up the pH value ?
what ions should I put in the solution?
The "pH" of your simulation is governed by the protonation state you assign to
each of the titratable residues in your protein or other molecules of interest.
There is no explicit representation of hydronium ions in the force fields
available in Gromacs. Furthermore, the presence of hydronium would require
acid-base chemistry (proton transfer) which is not possible under classical
mechanics force fields.
-Justin
Thank you
Lin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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