[gmx-developers] Inconsistency in Coulomb 1-4 energy term scaled by lambda

[Matt Wyczalkowski]

Yes, of course.  Its the potential, not the charge, which is scaled.

Sorry about the noise.

Matt

--
Matt Wyczalkowski
Doctoral Candidate, Biomedical Engineering
Pappu Lab: http://lima.wustl.edu
Washington University in St. Louis

On Wed, Feb 27, 2008 at 4:18 PM, David Mobley <dmobley at gmail.com> wrote:
> Matt,
>
>
>  > I am running some sanity checks on a system where I scale the charges
>  >  on a peptide in water.  Specifically, I can modify the charges in one
>  >  of two ways:
>  >  A) with free-energy = yes, and having lambda scale the charges
>  >  B) with free-energy = no, and modifying the charges directly in the
>  >  itp file.  To do this, I multiply the OPLS-AA charges by the factor
>  >  lambda, and write the modified itp file prior to processing with
>  >  grompp.
>  >
>  >  In principle, these two approaches should yield the same energies --
>  >  am I correct in assuming this?
>
>  I am not sure; you'll probably need to check the manual on how the
>  pairs are generated. In particular, one thing that I think makes this
>  complicated is the fact that usually you have a pairs list in your
>  topology file that specifies 1-4 interactions, but this doesn't state
>  interaction parameters explicitly. Then GROMACS will go through and
>  "generate" (calculate) the pair interactions when you run grompp (see
>  the gen-pairs entry in the header in your force field itp file). It
>  all hinges on how these are calculated. If these are calculated from
>  the modified charges in the topology file (scenario B), then they may
>  not be the same as if they're calculated from the A and B states with
>  free energy on. What this means is that you would be taking a somewhat
>  different path through lambda space -- the endpoints are the same but
>  the path is somewhat different.
>
>  To put this another way, when you set up a topology file with
>  different A and B state charges and linear scaling, your path follows
>  V = (1-lambda)*V_0 + lambda*V_1. Note that this is *not* equivalent to
>  changing the charges: Intramolecular interactions scale as q^2, but
>  with this functional form they are only decreased linearly with
>  lambda.
>
>  On the other hand, if you modify the charges directly in the topology
>  file, then your Hamiltonian has a different functional form that is
>  not as easily written. But now you're turning off intramolecular
>  interactions with lambda^2  (q^2), and intermolecular interactions
>  (between your solute and the environment) with lambda (q). So
>  obviously your pathway is different.
>
>  If this is right, of course, then not only should you see significant
>  differences in the 1-4 energies, but also in the SR coulomb, and it
>  looks like you *are* seeing such differences, although you didn't
>  mention them.
>
>  You can of course check that this is not a problem by ensuring that
>  you get the same free energy using both pathways. Both are completely
>  fine, as far as I'm aware; they're just nonequivalent.
>
>  Best wishes,
>  David
>