Hi rama, actually MARTINI has been further improved to allow secondary structure change. The title is: *"Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides"*
and here there is a link to the paper: http://dx.doi.org/10.1021/ct200876v Francesco 2012/10/10 XAvier Periole <[email protected]> > > Nope, but on other softwares. > > > On Oct 10, 2012, at 2:50 PM, rama david wrote: > > Thank you for your reply, >> >> Are these Cg can be used in Gromacs. >> >> Thank you in advance. >> >> With best wishes and regards, >> >> Rama david >> >> On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole <[email protected]> wrote: >> >> >>> Martini FF cannot model changes in secondary structure ... other CG FF >>> can. You'll find them easily in the literature. Notably the ones from >>> Deserno or Derreumaux. >>> >>> >>> On Oct 10, 2012, at 2:03 PM, rama david wrote: >>> >>> Hi friends, >>> >>>> >>>> I planed to use the martini force-field for my simulation study of >>>> peptide. >>>> >>>> The peptides are initially alpha-helix in nature. As they come together >>>> they formed amyloid fibre( Antiparallel Beta structure). >>>> >>>> Is it is possible to study the secondary structure backbone study by >>>> martini force field.???? >>>> >>>> I read in there tutorial that the Secondary structure is predefined >>>> therefore they are statics through out the simulation. >>>> Conformational changes that produces changes in Sec structure are out >>>> of >>>> scope in martini. only tertiary structure are free defined to change.. >>>> >>>> >>>> So what to do ??? >>>> How to use Martini FF to study secondary structure ??? >>>> >>>> Is there any way to use coarse grained FF to use for study in Sec. >>>> structure??? >>>> >>>> >>>> With Best wishes and regards, >>>> Rama David >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>> posting! >>>> * Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected]. >>>> * Can't post? Read >>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use thewww >>> interface or send it to [email protected]. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
