Re: [gmx-users] coarse grain dynamics
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
[gmx-users] coarse grain dynamics
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 -- gmx-users mailing listgmx-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
Re: [gmx-users] coarse grain dynamics
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 listgmx-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
Re: [gmx-users] coarse grain dynamics
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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] coarse grain dynamics
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.eduwrote: 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 listgmx-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 -- 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 listgmx-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 listgmx-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
Re: [gmx-users] coarse grain dynamics
thanks, but i am using gromacs version 4.0.07 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] coarse grain dynamics
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 listgmx-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 -- 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 listgmx-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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] coarse grain dynamics
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 listgmx-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 -- 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 listgmx-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 listgmx-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 -- 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
Re: [gmx-users] coarse grain dynamics
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 --
Re: [gmx-users] coarse grain dynamics
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 listgmx-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 -- 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 listgmx-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 listgmx-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
