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 ...
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 > -- 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