[gmx-users] solvent except water
Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! -- 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] solvent except water
leila karami wrote: Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! WHat do you mean? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] solvent except water
Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami -- 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] solvent except water
leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] solvent except water
Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] solvent except water
rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] solvent except water
David van der Spoel wrote: rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. There are even how-to's on the Gromacs site to accomplish this: http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-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/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 mailto: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
