2013/6/5 <[email protected]>: > > > 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 > > 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]. > 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.
