On 03/07/2013 06:13 PM, Christoph Junghans wrote: Hi Peter,
sorry for the late reply - I was on vaccation. I think Christoph is right. I just would like to add that the factor 5 in the tutorial is because the pressure corrected CG water is used, which has a factor 5 higher compressibility. Also, it is generally valid that for spherical adress setups a smaller prefactor is necessary for stability reasons. Let me know if you have further questions about this. I will update the manual to include the mass in the prefactor. Best, Sebastian > Hi Peter, > > sorry for the wait, I had to refresh my mind on how the prefactor is > calculated. Sebastian is the expert for this, so maybe he can comment > of my reply. > > I believe the number in tutorial scaled by a factor 5 as the > post-update scale function was not working at the time when we created > it. > Most of the time you will have to scale the prefactor in the iteration > for stabilization purposes. > > The manual was referring to small f, which is the "force per mass" and > rho as the number density (I will clarify that in the manual later). > So a more up-to-date definition see Eq. 3 of > <http://dx.doi.org/10.1021/ct200706f> or Eq. 8 of > <http://dx.doi.org/10.1103/PhysRevLett.108.170602>. > > Anyway, how is the prefactor calculated? (This now all in Gromacs > units, for Espresso the prefactor will be different) > > F has unit kJ/mol/nm, the density calculated by csg_density has the > unit u/nm^3, so the gradient of rho has unit u/nm^4 and hence the > prefactor will has unit kJ nm^3/mol/u (could be simplified) > > rho ~ 600 u /nm^3 > kappa_T = 4.5e-5 *1/bar = 7.5e-4 mol nm^3/kJ > > The prefactor would be > m_mol/kappa_T/rho^2= 18u/(7.5e-4 mol nm^3/kJ*(600 u/nm^3)^2 = 0.067 kJ > nm^3/mol/u > > I hope that helped. > > Cheers, > > Christoph > > 2013/3/6 Alexander Peyser <[email protected]>: >> We've been reproducing the hybrid thermoforce coupling we've seen in a few >> papers for AdRess, and we came to wonder about the thermoforce precoupling >> factor. >> >> According to the votca documentation, eq 7.4, this is 1/(\rho^2*k_t). >> The value in the tutorials in votca, the value of 0.01382 for spc. >> When we've tried to calculate this value, we come up with 1.26 in internal >> gromacs units, which we believe to be kJ * nm^3 * mol^-1, derived from the >> pressure units of gromacs of kJ/mol/nm^3, and k_t being the compressibility >> of 4.5 * 10^-5 / bar. >> >> Which units were used in deriving the value of 0.01382? Are we using the >> correct value for k_t? >> >> Regards, >> Alex Peyser >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/votca?hl=en. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
