[gmx-users] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin)
fileti at ufabc.edu.br
Thu Mar 19 11:02:56 CET 2009
Hello Berk and Justin. Thanks for the help.
In fact I was not using hardcore for electrostatic interactions
and also had a silly error in my topology. I fix everything and
now is working perfectly, without the giant peak near lambda = 0.
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170 Santo André - SP Brasil
On Wed, Mar 18, 2009 at 11:44 AM, Eudes Fileti <fileti at ufabc.edu.br> wrote:
> Berk Hello, thank you for your attention.
> My system has 24 hydroxyl groups, and in ethanol, there should be more than
> 20 solute-solvent hydrogen bonds
> being erased simultaneously (not to mention the possible intramolecular
> I did the simulation using the following protocol:
> 1) I made disappear the electrostatic interactions turning off the charges
> (by 200ps),
> 2) At the sequence I made disappear the LJ interactions (for more 200ps)
> 3) Finally I performed a run of 0.5ns.
> Do you think I should extend further the time of the simulations?
> This will solve the huge peak at lambda = 0?
> One more thing. Sorry, but so far I can not understood the reason
> for not to use sc-power=2, which in this case can reduce dramatically
> the errors associated with the integral of dG/dlambda.
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC
> Rua Santa Adélia, 166 - Bloco B, Sala 1048
> 09210-170 Santo André - SP Brasil
> skype: eefileti
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