From: jsachs_at_mail.csb.yale.edu
Date: Tue Feb 28 2006 - 10:00:13 CST
That's what I did in my BJ publication on ion/mmebrane interactions (Sachs et
al, Biophysical J. 2004), though I did it with CHARMM and in water, it worked
fine...so that's also what I recommend...Jonathan
Quoting Jérôme Hénin <jerome.henin_at_uhp-nancy.fr>:
> Jawahar,
>
> In your case, the dual-topology approach may not be the best-suited, because
> the partly environment-decoupled ions are free to wander about the simulation
> box and clash with the solvent.
>
> What you could do is emulate a "single-topology" perturbation by keeping both
> your ions fixed (NAMD fixedAtoms), in the very same position. (Disclaimer:
> although I can see no reason why it should fail, I have never tried that sort
> of trick).
>
> Please let us know how it works.
>
> Best,
> Jerome
>
>
> Le Samedi 25 Février 2006 07:40, Jawahar Neelankatan a écrit :
> > Hello,
> > I had a few questions about alchemical free energy perturbation
> > simulations. I am getting strange and inconsistent results for an
> > alchemical free energy perturbation simulation that I'm doing. I am
> > transforming a K+ ion to an Na+ ion in a box of ~200 methanol molecules
> > (solvent). So basically the only atoms involved in the transformation in
> > the FEP simulation are K (initial state, vanishing) and Na (final state,
> > appearing) and thus they are prevented from interacting with each other by
> > a modification (exclusion list) I made in the !NNB (non-bonding) section of
> > the psf file, using the alchemify program. The K and Na ions are however
> > allowed to interact with the bulk solvent (methanol) molecules. I also have
> > a .fep file defined that contains the ~200 methanol molecules, K ion and Na
> > ion. I wasn't sure whether to give both K and Na ions the exact same
> > coordinates or not. I didn't think it'd make a difference since they aren't
> > interacting to begin with. I went ahead and gave both of them the exact
> > same coordinates in the .fep file. I then ran a 10000 step (2 fs per step)
> > simulation with 5000 steps for equilibration and 5000 steps for sampling. I
> > made delta_lambda = 0.025 to allow 40 windows for the growth of lambda from
> > 0 to 1. The results I get don't bear much similarity to experimental
> > results and in the .fepout output file, I'm seeing a few unrealistically
> > large values (999999999) for the vdW(l+dl) i.e. the van der Waals energy
> > for the lambda2 state in each window. Is this normal ? I modified the .fep
> > file so that K and Na don't have the same coordinates (as they did in the
> > first simulation) but then I get the 'constraint failure in RATTLE
> > algorithm' error. However, I inserted a 'minimize 1000' command to minimize
> > the system before equilibrating and subsequently sampling and that error
> > doesn't occur anymore but I still get a few unrealistically large values
> > for vdW(l+dl) and erroneous values for dG.
> >
> > The configuration file and a small section of the .fep file are attached to
> > this email. Does it matter that I'm using the OPLS force field ? Any
> > suggestions are welcomed. Thanks.
> >
> > -Jawahar
> >
> >
> >
> >
> >
> >
> >
> > ---------------------------------
> > Yahoo! Mail
> > Use Photomail to share photos without annoying attachments.
>
> --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 91 Fax : (33) 3 83 68 43 87
> http://www.edam.uhp-nancy.fr/
>
>
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