[gmx-users] Free energy of transfer with accuracy

[David Mobley]

Chris,

> "Also, if your C60 is hollow, I can imagine that it might
> exclude solvent atoms from the inside, in which case you are going to
> have a big convergence issue as solvent begins to interpenetrate with
> the C60, which may lead to "noise" problems when this starts to
> happen, whatever soft core functional form you use. This just means
> you will need to run longer simulations in this regime."
>
> Which makes sense. Do you know a reference for this phenomenon?

Er, no. You can reference a personal communication from me saying that
my data suggests this is likely. :) Personal experience tells me that
this would probably be the case but I haven't ever seen a publication
on this.

David

David Mobley, Ph.D.
Assistant Professor of Chemistry
University of New Orleans
New Orleans, LA 70148
dlmobley at uno.edu
Office 504-280-6445
Fax 504-280-6860

> Thanks,
> Chris.
>
> -- original message --
>
> Eudes,
>
> On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti <fileti at ufabc.edu.br> wrote:
>
> [Hide Quoted Text]
> Hello David, thanks for the reply!
> I am simulating the free energy of transfer of the C60, from ethanol to
> benzene.
> The softcore parameters, I used the are the same values of Tieleman et.al.
> (nature nanotechnology, 3, 363).
> At figure, each curve refers to a different solvent; one of them for ethanol
> and another for benzene.
> For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1,
> turn off.
> I have found a large difference when simulating my system using sc_power=2.
> See in this link ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg )
> the comparison between
> plots from sc_power=1 and sc_power=2 for solute in benzene.
> Near 0 and 1, I believe that problem cancels out at difference, as can seen
> at
> ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ) . Then the main
> problem, in my view,
> is in the intermediate region, where the plot presents a deep (-500 units)
> and noise minimum.
> Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the
> critical region,
> one that makes the difference in calculation of the transfer free energy,
> remains the same,
> ie, the derivative still oscilates a lot and is not smooth.
> Are you believe that changing the value of alpha from 0.47 to 0.50 can
> resolve this?
> OK, there are several issues here.
> 1) The "noisy" minimum in dV/dlambda
> 2) The overall shape of dV/dlambda
> 3) Other potential problems
>
> On (1), the noisiness of the minimum you refer to really means there
> are convergence problems for some reason -- probably correlation times
> are particularly long there. This may be helped by using the soft core
> parameters I mention, but I am not sure. See item #3.
>
> On (2), in general, the overall shape of dV/dlambda seems to be
> smoothest and best behaved with the particular soft core parameters I
> mention. We did a lot of testing on this (i.e., many values of alpha
> at each of several sc-power values).
>
> On (3), there are other thing that can go wrong when using soft core.
> See http://www.alchemistry.org/wiki/index.php/Best_Practices for some
> discussion, and see rule #2 in particular. If you have any partial
> charges on atoms in your C60 this could be a potential source of error
> and noise. Also, if your C60 is hollow, I can imagine that it might
> exclude solvent atoms from the inside, in which case you are going to
> have a big convergence issue as solvent begins to interpenetrate with
> the C60, which may lead to "noise" problems when this starts to
> happen, whatever soft core functional form you use. This just means
> you will need to run longer simulations in this regime.
>
> Anyway, long story short, I suggest two things: (a) Make sure you turn
> off partial charges on C60 (without using soft core) before turning
> off the LJ using soft core, and (b) use the soft core functional form
> I suggest.
>
> David
>
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