Re: [gmx-users] Adding polarizability
David, As Mark answered there is no out of thebox polarizability. AFAIK there is no complete force field like that in Amber either, only Tinker has one. Just to clarify here, AMBER has an implementation of AMOEBA, Jay Ponder's polarizable force field that is also implemented in Tinker. So yes, there is a polarizable force field in AMBER. David ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding polarizability
David Mobley wrote: David, As Mark answered there is no out of thebox polarizability. AFAIK there is no complete force field like that in Amber either, only Tinker has one. Just to clarify here, AMBER has an implementation of AMOEBA, Jay Ponder's polarizable force field that is also implemented in Tinker. So yes, there is a polarizable force field in AMBER. Interesting, does that include all the multipoles and buffered 7-14 potentials etc? -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding polarizability
David, Interesting, does that include all the multipoles and buffered 7-14 potentials etc? Yes. My understanding is that the implementation is somehow separate from the main AMBER implementation and actually requires a copy of Tinker to set up the input files, but this may have changed (I haven't used it). You'll probably have to see the AMBER manual for details. Thanks, David -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adding polarizability
Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? Thank you, -- ~Eric Shamay ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding polarizability
Eric Shamay wrote: Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? As Mark answered there is no out of thebox polarizability. AFAIK there is no complete force field like that in Amber either, only Tinker has one. Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? there is flexspc.itp with this model. There is also TIP4P/Flex. Thank you, -- ~Eric Shamay ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding polarizability
Eric Shamay wrote: Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? GROMACS only does polarizability using shell functions (see various sections of the GROMACS manual), and there's no out-of-the-box AMBER equivalence implemented. Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Don't know. Please put different subjects in a different email, so that people can usefully use the email subject line to discard emails of no interest to them. This means you increase your chances that someone who knows your answer will read your email :-) Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? Don't know. Chapters 45 of the manual treat such topics, if they can be treated. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
