2013/6/3 <[email protected]>: > Dear Votca Users, > > I wish to reproduce my atomistic simulation angles of my protein with CG > between beads of residues. However I wish not to produce tables as an input > to gromacs mdrun but get the equilibrium value and then adjust the spring > constant to make it faster. Tabulated vs functional form is at most 50% faster, but the bonded interactions usually take 10% or less of the total simulation time, so you will not gain much in the end.
> For this purpose shall I just create distributions or histograms normalized > over the volume? Then place my spring where the distribution is max so set > angle in gromacs to this value and adjust the force constant to match this > distribution? Please, advise whether I am right. You will have to use the volume normalize histogram, but csg_boltzmann can do most of the calculation for you. Why don't you just take the table and fit k*(x-x_0)^2 to it? Cheers, Christoph > > Steven > > -- > 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.
