Hi Marc-André, Sikandar is 100% right. The main problem is that all currently implemented methods have a tabulated (step-wise constant) potential as outcome.
We are working on implementing the simplex algorithm, which can use arbitrary functional forms of the potential, but I can not guarantee that it will be finished soon. Cheers, Christoph 2011/9/2 Sikandar Mashayak <[email protected]>: > Hi > Marc-André > > One way to determine LJ potential energy terms is to first obtain CG > potential using IBI or IMC method and then fit 12-6 LJ functional form to > it. Of course, the quality of fit would depend upon whether the CG potential > has the LJ type shape or not. > > -- > sikandar > > On Fri, Sep 2, 2011 at 12:35 PM, Marc-André Dubois <[email protected]> > wrote: >> >> Hi guys, >> Is there a way to obtain The Lennard-Jones potential energy >> terms for the interaction between 2 CG beads from the radial distribution >> function? Thank you, >> >> Marc-André >> >> Le 2011-09-01 à 12:21, Marc-André Dubois a écrit : >> >> > Victor, >> > I appreciate your answer. Basically, one goal of this >> > investigation is to reproduce some of the amphiphilic behavior of a >> > molecule >> > that we have synthesize here in the lab. We would like to simulate the >> > transition from a aqueous environment to an apolar one and the conformation >> > change of our molecule to better understand the mechanism of these types of >> > molecules. The first idea was to use MARTINI to do this, so we tried using >> > this tool, and we get some results but we would like to construct a more >> > accurate coarse grained representation of the studied molecule. >> > >> > I will se the literature that you have propose. Thanks for your help, >> > >> > Marc-André >> > >> > >> > Le 2011-09-01 à 12:02, Victor Ruehle a écrit : >> > >> >> Dear Marcc-André, >> >> >> >> are you now just asking about the technical aspect, or about the >> >> method itself? If the latter, there is no clear answer to your >> >> problem. There are various methods available. The first question you >> >> should ask yourself is what kind of properties you want to reproduce >> >> in with your coarse-grained model. >> >> >> >> Most methods implemented in VOTCA are structure based approaches (or >> >> closely related to it) and therefore will most probably do wrong on >> >> thermodynamics. You can e.g. check the VOTCA references >> >> (http://www.votca.org/citations), there are also lot's of references >> >> given in the papers for more details on the method or links to other >> >> methods. That's still an incomplete list, but might be a good point to >> >> start with. >> >> >> >> If you want to act on the rdfs, I would start with IBI (see section in >> >> the manual). Otherwise, also force-matching or a hybrid approach might >> >> be worth a try. It's not yet officially supported in VOTCA, but >> >> depending on your system, it might be worth to have a look at what the >> >> MARTINI force field people did. >> >> >> >> Don't hesitate to ask any further questions, but providing some more >> >> details might help... >> >> >> >> Best, >> >> Victor >> >> >> >> 2011/9/1 Marc-André Dubois <[email protected]>: >> >>> Hi all, >> >>> I tried to follow the tutorials that you provide on your >> >>> website. Coarse-grained models are not actually the biggest concern of my >> >>> group, so I have to start from the basis. As I actually understand the >> >>> thing, I have to: >> >>> >> >>> 1. constructs an atomistic representation of the system, which will >> >>> give to you data to construct the coarse grained representation. >> >>> 2. runs a molecular dynamic at the atomistic scale >> >>> 3. obtains the radial distribution function for each of your CG beads >> >>> >> >>> From step 1 to step 3, I think that everything works fine. From these >> >>> steps, how it is possible to find the actual interaction potentials of >> >>> the >> >>> CG beads to constructs a forcefield that GROMACS will understand? I am >> >>> sorry >> >>> that this question would seems trivial, but as I previously said, I am >> >>> not >> >>> familiar with these kind of experiments. Thank you, >> >>> >> >>> Marc-André Dubois >> >>> >> >>> -- >> >>> You received this message because you are subscribed to the Google >> >>> Groups "votca" group. >> >>> To post to this group, send email to [email protected]. >> >>> To unsubscribe from this group, send email to >> >>> [email protected]. >> >>> For more options, visit this group at >> >>> http://groups.google.com/group/votca?hl=en. >> >>> >> >>> >> >> >> >> -- >> >> You received this message because you are subscribed to the Google >> >> Groups "votca" group. >> >> To post to this group, send email to [email protected]. >> >> To unsubscribe from this group, send email to >> >> [email protected]. >> >> For more options, visit this group at >> >> http://groups.google.com/group/votca?hl=en. >> >> >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "votca" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group at >> > http://groups.google.com/group/votca?hl=en. >> > >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/votca?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > -- Dr. Christoph Junghans Votca Core Developer Web: http://www.votca.org -- You received this message because you are subscribed to the Google Groups "votca" group. 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