Re: [gmx-users] force field parameters for Fe3O4?
On 4/13/18 6:26 AM, rose rahmani wrote: Hello, I use AMBER force field. So, how about periodic structures? like inorganic nanosheet and nanotubes? One would never attempt to do parametrization directly on a full, periodic structure, largely because (1) it's not possible/practical and (2) you will end up with a non-transferable, geometry-dependent solution to the charge distribution in QM. A large structure must be parametrized from a smaller repeating unit that reflects a suitable building block of the whole thing, using an appropriate level of QM theory that is consistent with the methodology of the force field you've chosen. If you parametrize parts of a force field with different levels of theory, you get a hodge-podge force field with no guarantee of functionality. -Justin Thank you so much On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote: Hello, this depends on the force field you are using. Some of them use parameters from a QM optimization and partial charge calculation. But even then you need to be careful that the results from the QM are not just random numbers :) But I'm not sure myself how I would tackle something like Magnetite right now, as it would also require obtaining parameters for the LJ interactions. Cheers! On 13/04/18 12:13, rose rahmani wrote: On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: Hello, I would recommend that you check relevant publications for the simulation of magnetite if people have tried to simulate it in solvent. I could not find anything during a short search, but maybe you'll be more successful. :) If there are no published parameters in the literature you will have to parametrize the molecule yourself according to the method used by the force field you are using. I would look at the section in the user guide dealing with this ( http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields ) Is it true to optimize the molecule for example in gaussian(dft)first, and then calculate the charges and make an .itp file for it?is it always reliable? and then at the documentation for your force field! Cheers! On 13/04/18 11:21, leila karami wrote: Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field parameters for Fe3O4?
Hello, I use AMBER force field. So, how about periodic structures? like inorganic nanosheet and nanotubes? Thank you so much On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote: > Hello, > > this depends on the force field you are using. Some of them use > parameters from a QM optimization and partial charge calculation. > But even then you need to be careful that the results from the QM are > not just random numbers :) > > But I'm not sure myself how I would tackle something like Magnetite > right now, as it would also require obtaining parameters for the LJ > interactions. > > Cheers! > > On 13/04/18 12:13, rose rahmani wrote: > > On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > > > >> Hello, > >> > >> I would recommend that you check relevant publications for the > >> simulation of magnetite if people have tried to simulate it in solvent. > >> I could not find anything during a short search, but maybe you'll be > >> more successful. :) > >> If there are no published parameters in the literature you will have to > >> parametrize the molecule yourself according to the method used by the > >> force field you are using. > >> I would look at the section in the user guide dealing with this > >> ( > >> > http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields > ) > >> > >> > > Is it true to optimize the molecule for example in gaussian(dft)first, > and > > then calculate the charges and make an .itp file for it?is it always > > reliable? > > > >> and then at the documentation for your force field! > >> > >> Cheers! > >> > >> On 13/04/18 11:21, leila karami wrote: > >>> Dear gromacs users, > >>> > >>> I want to simulate a protein in different concentration of Fe3O4. > >>> > >>> How to obtain force field parameters of Fe3O4? > >>> > >>> Any help will highly be appreciated. > >>> > >>> Best, > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field parameters for Fe3O4?
Hello, this depends on the force field you are using. Some of them use parameters from a QM optimization and partial charge calculation. But even then you need to be careful that the results from the QM are not just random numbers :) But I'm not sure myself how I would tackle something like Magnetite right now, as it would also require obtaining parameters for the LJ interactions. Cheers! On 13/04/18 12:13, rose rahmani wrote: On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: Hello, I would recommend that you check relevant publications for the simulation of magnetite if people have tried to simulate it in solvent. I could not find anything during a short search, but maybe you'll be more successful. :) If there are no published parameters in the literature you will have to parametrize the molecule yourself according to the method used by the force field you are using. I would look at the section in the user guide dealing with this ( http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields) Is it true to optimize the molecule for example in gaussian(dft)first, and then calculate the charges and make an .itp file for it?is it always reliable? and then at the documentation for your force field! Cheers! On 13/04/18 11:21, leila karami wrote: Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field parameters for Fe3O4?
On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > Hello, > > I would recommend that you check relevant publications for the > simulation of magnetite if people have tried to simulate it in solvent. > I could not find anything during a short search, but maybe you'll be > more successful. :) > If there are no published parameters in the literature you will have to > parametrize the molecule yourself according to the method used by the > force field you are using. > I would look at the section in the user guide dealing with this > ( > http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields) > > Is it true to optimize the molecule for example in gaussian(dft)first, and then calculate the charges and make an .itp file for it?is it always reliable? > and then at the documentation for your force field! > > Cheers! > > On 13/04/18 11:21, leila karami wrote: > > Dear gromacs users, > > > > I want to simulate a protein in different concentration of Fe3O4. > > > > How to obtain force field parameters of Fe3O4? > > > > Any help will highly be appreciated. > > > > Best, > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field parameters for Fe3O4?
Hello, I would recommend that you check relevant publications for the simulation of magnetite if people have tried to simulate it in solvent. I could not find anything during a short search, but maybe you'll be more successful. :) If there are no published parameters in the literature you will have to parametrize the molecule yourself according to the method used by the force field you are using. I would look at the section in the user guide dealing with this (http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields) and then at the documentation for your force field! Cheers! On 13/04/18 11:21, leila karami wrote: Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] force field parameters for Fe3O4?
Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
