On 11/1/13 8:39 AM, xiao wrote:
It is impossible. But you can add proton to the acidic amino acid.
It's certainly not impossible. There are constant-pH methods that exist; the
list archive contains many posts on this topic, and more information can be
found at:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
Whether or not you can easily accomplish such simulations in Gromacs is another
matter.
Standard MD does not allow for dynamic protonation states, so the closest you
can get without running more advanced MD is to use fixed protonation states,
assigned by pdb2gmx, that are indicative of the most prevalent state of the
residues at a given pH value.
Changing ionic strength is trivial; that's what genion -conc is for.
-Justin
At 2013-11-01 20:36:41,Mass <masstransfer_2...@yahoo.com> wrote:
Dear Gromacs users,
Just was wondering if it is possible to protein solution let say Lysozyme in
Water example of Justin tutorial at different pH and ionic strengths, if so how?
Thanks
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Justin A. Lemkul, Ph.D.
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