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 2013/6/7 <[email protected]> > > > 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]. > 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.
