Chih-Ying Lin wrote:
Hi
Does the Gromacs set the default pH = 7.0 ?
No.
This also isn't a meaningful question for an explicit-solvent
simulation. If you'd done the calculation I suggested yesterday
(http://www.gromacs.org/pipermail/gmx-users/2009-May/042128.html) then
you'd already appreciate that.
You've had a number of suggestions from well-meaning people that perhaps
you need to do some serious background reading. While several people
here are happy to give free help with general GROMACS issues, asking
questions on this list is not an effective replacement for knowing
undergraduate-level coursework material, reading molecular simulation
textbooks, doing molecular dynamics tutorials, reading primary
literature and experimenting with calculations. We got our knowledge
doing the above, and it's not the job of anybody here to teach it to
you. :-)
Mark
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