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.
