[gmx-users] Toy input system - MD simulation
Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Toy input system - MD simulation
On 1/9/13 6:25 AM, Maria Astón Serrano wrote: Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? You can find a large number of common molecules (both coordinates and topologies) on http://virtualchemistry.org/. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Toy input system - MD simulation
On 2013-01-09 12:25, Maria Astón Serrano wrote: Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
