On 9/6/12 11:27 AM, [email protected] wrote:
Ah okey.
Thank you for the helpful answer.
In some cases it can also be that the phosphate is not protonated at all.
Does gromacs also recognize that a proton at this position would make no
sense and remove it from the structure?
No. Gromacs does what you tell it. If your topology has a proton, the
simulation is carried out as such.
-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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