[gmx-users] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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
[gmx-users] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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
[gmx-users] GPCR MD Tutorial Using GROMACS (URL)
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban On Thu, Apr 26, 2012 at 3:08 PM, Albert mailmd2...@gmail.com wrote: it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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 -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert mailmd2...@gmail.com wrote: Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert mailmd2...@gmail.com wrote: Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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
