W dniu piątek, 7 czerwca 2013 11:46:59 UTC+1 użytkownik Victor Rühle napisał: > > Dear Steven, > > that sounds correct. yes, the output is in kJ/mol for csg_boltzmann. the > 3rd column is the force which was calculated using finite differences and > is needed for tabulated potentials. If you fit you can just ignore the 3rd > column. Be aware that your angle distribution can have multiple minima and > not necessarily have a harmonic shape. > > In any case, I recommend to run a cg simulation with your new potential > and compare the distributions (they should match the atomistic ones) as > well as cross correlations e.g. using a 2D histogram (these can be > problematic). Failing to reproduce cross correlations of e.g. angle and > dihedrals can lead to a wrong stiffness / end-end distance and overall > shape. > > Victor >
Thank you for this. Indeed, my angle distributions and potentials have two minima but quartic potential (implemented in Gromacs) fit them very well. I will compare my results once finished my CG force field. Steven > > > 2013/6/7 <[email protected] <javascript:>> > >> >> >> 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] 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<http://groups.google.com/group/votca?hl=en>. >>>> > >>>> >>>> > For more options, visit >>>> > https://groups.google.com/**groups/opt_out<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 votca+un...@**googlegroups.com. >>> To post to this group, send email to [email protected]. >>> Visit this group at >>> http://groups.google.com/**group/votca?hl=en<http://groups.google.com/group/votca?hl=en> >>> . >>> For more options, visit >>> https://groups.google.com/**groups/opt_out<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. >> >> >> > > -- You received this message because you are subscribed to the Google Groups "votca" group. 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