W dniu środa, 5 czerwca 2013 08:55:46 UTC+1 użytkownik Emiliano Brini napisał: > > Dear Steven, > > On Jun 4, 2013, at 10:26 AM, [email protected] <javascript:> wrote: > > > > On Monday, June 3, 2013 4:26:29 PM UTC+1, Christoph Junghans wrote: >> >> 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? >> > > 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 ? > > > > In the Gromacs topology file you write the parameters of the potential > functions, therefore you need to fit the potential curve. >
Thank you again, Please correct me if I am wrong: I take the output from the csg_boltzmann given with option tab so tabuated potential. Then I convert rad to deg and I can fit my curve with k*(x-x_0)^2. That means that the output potential is in kJ/mol? What is the 3rd column in this output? Steven > > >> 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 > > > It is quite normal for CG distributions to not be gaussian. Since the CG > system has less degrees of freedom compared to the atomistic one, a single > CG bonded interaction represent by its nature several atomistic > intramolecular interactions (bonds, angles, dihedrals, and intramolecular > non bonded interaction). Even more a simple Boltzmann inversion of a > distribution can cast into the potentials contributions coming from parts > of the molecule (or of the system) that do not belong to the group of atoms > that you are directly considering. Therefore the distributions you obtain > are a sum of contributions each one with its own weight. It is extremely > difficult to say a priory something about the shape of the final > distribution. > As it has been said the use of a table normally is not too expensive, > therefore it is normally a good idea to use them. > Anyhow the best thing you can do is to run two test system: one where you > use tabulated potential and one where you use your "best" fitting. In this > way you can see the difference between their performances and their results > in your specific case. > > Cheers, > > Emiliano > > > >> > >> > 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] <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. > > > > > -- 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.
