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? 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.
