thanks all for the discussion.
On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Thanks for the comments and info, but is there any way to take a >> particular frame for eg. the last frame of CG simulation and extend >> the run into all-atom simulation further ... >> > > There are tools out there to reconstruct an atomistic representation of a CG > system (see link below, and poke around Google for a few minutes). If you > want to start a whole new simulation, that is certainly possible after (of > course) regenerating your system topology to match the new system. > > -Justin > >> On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson >> <thomp...@purdue.edu> wrote: >>> >>> I agree with Justin on this one. Simulations run using CG that is not >>> optimized >>> for reconstruction may not actually reflect the type of interactions you >>> are >>> looking for. The current result of this simulation may not directly >>> correspond >>> to a full atomistic result, so even if a reconstruction were performed >>> you would >>> most likely NOT be able to draw conclusions from it. >>> >>> Otherwise, everyone would run really fast simulations in CG, then >>> reconstruct >>> their systems afterward. :) >>> >>> >>> >>> Quoting "Justin A. Lemkul" <jalem...@vt.edu>: >>> >>>> >>>> ram bio wrote: >>>>> >>>>> thanks, >>>>> >>>>> but i am using gromacs version 4.0.07 >>>>> >>>> I think the general consensus thus far is you won't be able to do what >>>> you >>>> want >>>> without significant effort to reconstruct your system, and perhaps then >>>> you >>>> should question whether any tools that seek to build optimal hydrogens >>>> from >>>> CG >>>> structures are going to bias the result. Would those hydrogen bonds >>>> have >>>> actually formed in an AA simulation? Hard to tell. If you want to >>>> analyze >>>> hydrogen bonds, CG approximations are not probably sufficient. >>>> >>>> This is a good exercise in planning your analysis before conducting your >>>> simulation. You can probably estimate some sort of polar contacts from >>>> your >>>> CG >>>> representation, but not hydrogen bonds. >>>> >>>> -Justin >>>> >>>>> On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi >>>>> <egv...@gmail.com> wrote: >>>>>> >>>>>> Hi, >>>>>> To change between representations (atomistic <--> coarse grained), if >>>>>> you >>>>>> are using the MARTINI FF, you can use the modified version of Gromacs >>>> >>>> 3.3, >>>>>> >>>>>> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt >>>>>> If you don't want to switch to full-atomistic representation, check >>>>>> which >>>> >>>> CG >>>>>> >>>>>> atom types are able to form hydrogen bonds and look for interactions >>>> >>>> between >>>>>> >>>>>> them. Obviously, this will be an approximation. >>>>>> >>>>>> Esteban G. Vega-Hissi >>>>>> UNSL >>>>>> San Luis >>>>>> Argentina >>>>>> -- >>>>>> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson >>>> >>>> <thomp...@purdue.edu> >>>>>> >>>>>> wrote: >>>>>>> >>>>>>> There are programs around for reconstruction of full-atomistic >>>>>>> representations >>>>>>> from coarse-grained representations, however. I don't know if there >>>>>>> are >>>>>>> any >>>>>>> available for the GROMACS architecture. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Quoting Nuno Azoia <naz...@det.uminho.pt>: >>>>>>> >>>>>>>> Hi there! >>>>>>>> >>>>>>>> I never worked with coarse grain simulations, but if you used a >>>>>>>> coarse >>>>>>>> grain methodology you didn't include all the atoms, so you didn't >>>>>>>> included hydrogens. So now you can not see them, of course. They are >>>> >>>> not >>>>>>>> >>>>>>>> there. >>>>>>>> >>>>>>>> If you need to "know the hydrogen bond interactions" you need to do >>>> >>>> some >>>>>>>> >>>>>>>> "all atoms" simulation, not coarse grain. >>>>>>>> >>>>>>>> Nuno Azoia >>>>>>>> >>>>>>>> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: >>>>>>>>> >>>>>>>>> Dear Gromacs Users, >>>>>>>>> >>>>>>>>> I have done coarse grain simulation for 2 peptides in bilayer for >>>>>>>>> 1000ns, and now i would like to know the hydrogen bond interactions >>>>>>>>> between these two peptides. Please let me know how to do this, i >>>>>>>>> can >>>>>>>>> visualize the trajectory in VMD, but unable to calculate the >>>>>>>>> hydrogen >>>>>>>>> bonding distance and the hydrogen bonds existing.. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Ram >>>>>>>> >>>>>>>> -- >>>>>>>> Nuno Gonçalo Azoia Lopes >>>>>>>> >>>>>>>> Laboratório de Investigação em Acabamento >>>>>>>> Departamento de Engenharia Têxtil >>>>>>>> Universidade do Minho >>>>>>>> Campus de Azurém >>>>>>>> 4800-058 Guimarães >>>>>>>> Portugal >>>>>>>> >>>>>>>> Tel: +351 253 510 280 - Ext: 517 289 >>>>>>>> Fax: +351 253 510 293 >>>>>>>> >>>>>>>> Mobile: +351 965 382 487 >>>>>>>> E-mail: naz...@det.uminho.pt >>>>>>>> http://nazoia.net >>>>>>>> >>>>>>>> -- >>>>>>>> gmx-users mailing list gmx-us...@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 >>>>>>>> >>>>>>> -- >>>>>>> Jared James Thompson >>>>>>> Department of Medicinal Chemistry and Molecular Pharmacology >>>>>>> Laboratory for Computational Drug Design and Biology >>>>>>> RHPH 504C >>>>>>> Heine Pharmacy Building >>>>>>> 575 Stadium Mall Drive >>>>>>> West Lafayette, IN 47907-2091 >>>>>>> -- >>>>>>> gmx-users mailing list gmx-us...@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-us...@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 >>>>>> >>>> -- >>>> ======================================== >>>> >>>> Justin A. Lemkul >>>> Ph.D. Candidate >>>> ICTAS Doctoral Scholar >>>> MILES-IGERT Trainee >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> -- >>>> gmx-users mailing list gmx-us...@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 >>>> >>> >>> -- >>> Jared James Thompson >>> Department of Medicinal Chemistry and Molecular Pharmacology >>> Laboratory for Computational Drug Design and Biology >>> RHPH 504C >>> Heine Pharmacy Building >>> 575 Stadium Mall Drive >>> West Lafayette, IN 47907-2091 >>> -- >>> gmx-users mailing list gmx-us...@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 >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? 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