W dniu czwartek, 6 czerwca 2013 01:47:09 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/6/5 <[email protected] <javascript:>>: > > > > > > On Wednesday, June 5, 2013 10:41:10 AM UTC+1, [email protected] wrote: > >> > >> > >> > >> On Wednesday, June 5, 2013 8:55:46 AM UTC+1, Emiliano Brini wrote: > >>> > >>> Dear Steven, > >>> > >>> On Jun 4, 2013, at 10:26 AM, [email protected] 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. > >>> > >>>> > >>>> 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 > >> > >> > >> > >> And the other thing: does csg_boltmann with option tab produce > potentials > >> which can be an input (after extrapolation and smoothing) to straight > to > >> mdrun? I mean: Is Y value of the potential plot in kJ/mol and X value > of > >> radians (in case of angle)? > >> > >> Steven > >> > > As far as I know is not possible to prepare automatically table for > angular > > potentials, mainly because Gromacs needs degrees and Votca gives > radians. > > Normally I use Votca to calculate the distribution and then I convert > and > > invert it using the formulas in chapter 2.2 of the manual. > > > > Emiliano > > > > Thanks for this. csg_boltzmann divides the distribution by sin(teta) and > > provides the normalized volume potential. I will double check the > Gromacs > > input (radians or degrees) as the angular force constant is in kJ/mol > rad^2. > > > > Steven > > > > Can anyone can comment on this please? > The main problem is not the grad to rad conversion, that's trivial, > but the fact the bonded distributions might have regions with no data > in the middle of their range and then VOTCA cannot interpolate that > automatically. > > In general, VOTCA uses rad and gromacs uses degress, to account for > that we add a --r2d option (see $ csg_call convert_potential gromacs > --help) to > $ csg_call convert_potential gromacs > in the 1.3-dev version of VOTCA (use build.sh --dev to get it). > > You might also want to have a look at older threads on this mailing > list discussing that topic. > > Christoph >
Thank you for this. the last question: What is in the 3rd column of the resulted potential with csg_boltzmann and tab option? Steven > > > > > 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]. > >>>> > 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. > >>> > >>> > >>> > >>> > > -- > > 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.
