do you have these ion binding problems in MD of the endpoint state, or only
during TI?
is the ion that is binding too much the Na+ that you are disappearing? does
the binding happen when the Na is nearly disappeared?
these details will be important to understanding the problem. it's
likely that removing the vdw on the Na while it still has a charge will not
be easy, and need some special treatment with softcore functions.
On Tue, Mar 7, 2023 at 1:46 PM He, Amy via AMBER <amber.ambermd.org> wrote:
> Dear Amber community,
>
> I am running TI simulations with sander.MPI in Amber 20. My systems are
> all made of a simple dipeptide in explicit TIP3P waters + ions. These
> simulations are intended for baseline corrections of the TI simulations I
> have done for the protein systems, in which I transform the charge state of
> residues.
>
> I have a working TI protocol for the protein systems with similar setups.
> But I am having trouble getting reasonable DV/DL for these simple
> dipeptides. I got some very large (over 3000 kcal/mol) DV/DL because I
> cannot shield the charged side chain from binding with a counterion..
>
> Please see more details below about the simulation setups:
>
> The dipeptide is a glutamate residue capped on both sides: NME-GLU-ACE.
> The protonated form is: NME-GLH-ACE
>
> The initial state contains: NME-GLU-ACE, 4 Na+, 3 Cl-, about 23000 TIP3P
> waters
> The end state contains: NME-GLH-ACE, 3 Na+, 3 Cl-, same number of waters
>
> The atoms that undergo alchemical transformation are:
> OE2 and one Na+ in the initial state
> OE2 and HE2 in the end state
>
> I would really appreciate any comments/suggestions regarding this… Is it
> just a bad idea to transform a counterion (even though I have that delta G
> canceled in my thermodynamic cycle..)? Should I just exclude all Na+ to
> avoid the binding?
>
>
> Many Thanks,
> Amy
>
>
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
> he.1768.osu.edu<mailto:he.1768.osu.edu>
>
>
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Received on Tue Mar 07 2023 - 13:00:02 PST
