<div>Hello David, thanks for the reply! </div><div><br></div><div>I am simulating the free energy of transfer of the C60, from ethanol to benzene.</div><div>The softcore parameters, I used the are the same values of Tieleman <a href="http://et.al">et.al</a>. (nature nanotechnology, 3, 363). </div>
<div>At figure, each curve refers to a different solvent; one of them for ethanol and another for benzene. </div><div>For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1, turn off. </div><div><br></div>
<div>I have found a large difference when simulating my system using sc_power=2. </div><div>See in this link ( <a href="http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg">http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg</a> ) the comparison between </div>
<div>plots from sc_power=1 and sc_power=2 for solute in benzene.</div><div>Near 0 and 1, I believe that problem cancels out at difference, as can seen at </div><div>( <a href="http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg" target="_blank">http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg</a> ) . Then the main problem, in my view, </div>
<div>is in the intermediate region, where the plot presents a deep (-500 units) and noise minimum. </div><div>Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the critical region, </div><div>one that makes the difference in calculation of the transfer free energy, remains the same, </div>
<div>ie, the derivative still oscilates a lot and is not smooth.</div><div><br></div><div>Are you believe that changing the value of alpha from 0.47 to 0.50 can resolve this?</div><div>Please, ask me more details if you need.</div>
<div>Thanks again.</div><div>eef</div><div><br></div><div><br></div>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>
09210-170 Santo André - SP Brasil<br>+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Message: 4<br>
Date: Thu, 11 Dec 2008 07:24:26 -0600<br>
From: "David Mobley" <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>><br>
Subject: Re: [gmx-users] Free energy of transfer with accuracy<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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<br>
Hi,<br>
<br>
> Hi gmx-users,<br>
> I have tried to calculate the free energy of transfer of<br>
> a solute between two solvents by thermodynamic integration.<br>
> However, the dgdl plot I have obtained is not smooth enough to ensure<br>
> accuracy.<br>
> I have used a non homogeneous spacing for lambda. The first is from 0.0 to<br>
> 0.4 (dl=0.04),<br>
> the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1<br>
> (dl=0.04).<br>
> Overall, I was performed 40 simulations.<br>
> As can be seen in the figure (<br>
> <a href="http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg" target="_blank">http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg</a> ),<br>
> there is a large fluctuation in the region that goes from 0.40 to 0.48.<br>
> Each simulation was carried out by 0.5ns preceded by 0.15ns of<br>
> equilibration.<br>
> I am using soft-core whose parameters are:<br>
> ; Free energy control stuff<br>
> free_energy = yes<br>
> init_lambda = 0.00<br>
> delta_lambda = 0<br>
> sc_alpha = 1.3<br>
> sc-power = 1.0 (for this I also used 2).<br>
> sc-sigma = 0.47<br>
> In the example of the link sc-power=1, but I re-did the calculations with<br>
> sc-power=1<br>
> and I found the same behavior (although the format of the plot was a little<br>
> different).<br>
<br>
> Can you suggest me a way to calculate this free energy difference with<br>
> accuracy?<br>
> The perturbation free energy method could give better results?<br>
> Thank you<br>
> EEF<br>
<br>
This does look alarming.<br>
<br>
I would make a couple comments here:<br>
1) Soft core parameters can be fairly sensitive. Michael Shirts and I<br>
have both looked at these independently and we find that sc-power =<br>
1.0 with an alpha of 0.5 is typically substantially better than most<br>
other options. Even alpha = 0.47 or 0.53 can be much worse than alpha<br>
= 0.5. Your dV/dlambda curve looks to me like your soft core values<br>
are far from ideal and that you are seeing a huge peak near lambda = 0<br>
for this reason.<br>
2) Am I interpreting your e-mail correctly that lambda = 0 corresponds<br>
to one solvent, and lambda = 1 corresponds to another? If so, I am<br>
unclear on how exactly you're doing the transformation and could use<br>
more detail on how you've set this up. A more straightforward (and<br>
easier?) way to do this would be to transfer the solute to vacuum from<br>
each solvent and then take the difference in the vacuum transfer free<br>
energies. Please clarify which you're doing so we can help better.<br>
<br>
<br>
David Mobley, Ph.D.<br>
Assistant Professor of Chemistry<br>
University of New Orleans<br>
New Orleans, LA 70148<br>
<a href="mailto:dlmobley@uno.edu">dlmobley@uno.edu</a><br>
Office 504-280-6445<br>
Fax 504-280-6860<br></blockquote></div>