If we follow strictly the parameterization guides, Urea has to be mapped to only one CG bead (because of reduction from 4 to 1), but I believe that this would not be able to represent properties of the molecule. Instead I would use a 2 beads model or try something like it has been done with water, i.e., more than one urea molecule to 1 or 2 beads. This is only an idea! Tell us about your results!!
Best Esteban -- 2010/5/11 XAvier Periole <x.peri...@rug.nl> > > There is no Urea topology for Martini FF. Would be very interesting to have > one! > > you need to look for some properties that you be able to reproduce. > have a look at the papers! > > Typically you need to find logP (partitioning data) between different > media and and reproduce it using some Martini bead type ... and in > the case of Urea you might need to define a new type ... > > XAvier. > > > On May 11, 2010, at 3:38 PM, Luca Mollica wrote: > > Dear all, >> I am looking for a urea topology for some CGMD simulations performed with >> the MARTINI FF. >> Actually I am planning to design it on my own, but in case at least a >> "source of inspiration" (I have found no papers about the issue) would be >> appreciated. >> Cheers, >> >> Luca >> >> >> >> -- >> >> ........................................................ >> >> -- >> >> >> >> Luca Mollica >> Protein Dynamics and Flexibility by NMR >> Institut de Biologie Structurale >> 41 Rue Jules Horowitz >> Grenoble >> 38027 >> France >> >> E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) >> >> Telephone: +33.438783889 >> >> >> -- >> >> >> Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack >> of cigarettes, it's dark, and we're wearing sunglasses. >> Jake: Hit it. >> >> (The Blues Brothers) >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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