From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jun 28 2021 - 15:07:39 CDT
C-termini and N-termini titrations are implemented, but not
parameterized. You would have to build the residues and find/compute
reference values yourself. The syntax is explained in the developer's
manual, but I'm not sure this ever got posted on the website (contact me
off-line if you are interested in a copy).
Unfortunately membrane simulations are an unsolved problem for
constant-pH MD in NAMD since they frequently produce massive PMF
artifacts. There are some post-hoc corrections (described in the paper),
but they can be cumbersome and may not work well for large systems with
many titratable residues.
On 6/28/21 9:02 AM, Diship Srivastava wrote:
> I am starting a constant ph md on a ph activated lipopeptide (lp)
> insertion into a lipid bilayer. Lp has 9 titrable residues. My
> questions are as follows:
> 1) I have applied a cter patch during psf generation. Since there is
> also a cter patch present in charmm 36 cph ff, will this also be
> included as a titrable part?
> 2) As lp inserts into the bilayer it's environment will change. How do
> I for that in cphmd?
> Thanks in advance.
> Diship Srivastava
> IIT(ISM) Dhanbad
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