On Monday, June 3, 2013 4:26:29 PM UTC+1, Christoph Junghans wrote: > > 2013/6/3 <[email protected] <javascript:>>: > > 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? > That is what I am planning to do.But which table? Shall I take the table with distributions of bonds (or angles?) of the potential or volume normalized histogram to fit k*(x-x_0)^2 ? > > Cheers, > > Christoph > > Thanks for your help. I got gaussian distribution for my bonds so I can fit it into k*(x-x_0)^2 and multiple gaussian distribution of my angles... Is that normal? My beads involve 7 - 22 atoms, maybe that is why? Shall I use a tables as an input to mdrun? Steven > > > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
