Re: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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
Fw: [gmx-users] ***using output of dl_poly in gromacs??***
Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated - Forwarded Message - From: David van der Spoel sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Sent: Wednesday, 26 June 2013, 11:10 Subject: Re: [gmx-users] ***using output of dl_poly in gromacs??*** On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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.se http://folding.bmc.uu.se/ -- 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/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_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: Fw: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-26 09:14, hamid mosaddeghi wrote: Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated for some analysis you do not need it at all. For some analysis you could also leave out the metal (e.g. secondary structure of protein). - Forwarded Message - *From:* David van der Spoel sp...@xray.bmc.uu.se *To:* gmx-users@gromacs.org *Sent:* Wednesday, 26 June 2013, 11:10 *Subject:* Re: [gmx-users] ***using output of dl_poly in gromacs??*** On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://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. mailto:gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] ***using output of dl_poly in gromacs??***
Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck -- 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
