[gmx-users] Free energy of protonation

[Sotirios Dionysios I. Papadatos]

My advise is a bit general.
Try the same process with a different molecule (one that can support this change), try the same molecule with an AA ff, since it is already done (as you mentioned) do you get similar results?
These tests might help you find out if there is something wrong with your mdp.
I haven't changed a bead in free energy so I am not 100% sure, but the few mdp options that you provided seem reasonable.
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Gmx QA <gmxquestions at gmail.com>
Sent: Wednesday, April 1, 2020 7:52 PM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] Free energy of protonation

Dear list,

I am trying to calculate the free energy for protonating a single monomer
of oleic acid with the martini forcefield. This in preparation for other
work, and I wanted to start by reproducing what is already done.

To do this, I have defined the following in my topology to describe the
change in protonation state going from A (protonated) to state B (charged).
The martini bead type needs to change as well in this process.

[ atoms ]

; id    typeA   resnr   residu  atom    cgnr    chargeA   massA typeB
chargeB massB

  1     P4      1       OAN     COO     1       0               Qa      -1

I also have this very simple mdp file for doing the transformation

free_energy              = yes

init_lambda-state        = 1

fep-lambdas              = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0


And I am using fep-lambdas to describe the entire process. With this, I can
run through grompp and mdrun with different values of init-lambda-state,
but the output I get in each case is the same for each different simulation.


I check this by


gmx analyze -f md.xvg -ee


And I always get the same value for the average. Is there something I am
missing or not specifying properly?


Thanks

/PK
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