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. Bests _______________________________________ 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 +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/
On Wed, Mar 18, 2009 at 11:44 AM, Eudes Fileti <[email protected]> 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 > HB's). > > 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 > +55.11.4437-8408 > skype: eefileti > http://cromo.ufabc.edu.br/~fileti/ > >
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