Re: [gmx-users] potential energy doesn't have negative value
Den 2020-03-15 kl. 00:59, skrev Justin Lemkul: On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin The baseline oof the potential energy is not a meaningful number in classical force fields. You have to subtract 100 times the energy of the monomer, then you will have the enthalpy of vaporization (+/- kT) which you can compare to experiment. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] potential energy doesn't have negative value
thank you so much Mr.justin Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:38, Justin Lemkul wrote: On 3/14/20 8:05 PM, Afsane Farhadi wrote: > what do I have to do for solving this mater? I want to use a opls as > forcefield. how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin > Sent from Yahoo Mail on Android > > On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: > > On 3/14/20 7:15 PM, Afsane Farhadi wrote: >> I generate a box of 100 molecules of methyldiethanolamine with >> insert-molecules command .I downloaded its itp file from ATB server. I think >> that forcefield is gromos . after an energy minimization the potential >> energy is positive. the mdp file is attached. > The mailing list does not accept attachments. > > ATB does produce GROMOS-compatible force fields, but it is always up to > the user to determine if the parameters are suitable. A positive > potential energy means that the intermolecular interactions are weak > compared to the intramolecular (bonded) interactions. You can use gmx > energy or look in the .log file to see the various contributions to the > total potential energy. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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. -- 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] potential energy doesn't have negative value
what do I have to do for solving this mater? I want to use a opls as forcefield. how can I find that forcefield for methyldiethanolamine? Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: On 3/14/20 7:15 PM, Afsane Farhadi wrote: > I generate a box of 100 molecules of methyldiethanolamine with > insert-molecules command .I downloaded its itp file from ATB server. I think > that forcefield is gromos . after an energy minimization the potential energy > is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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. -- 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] potential energy doesn't have negative value
On 3/14/20 8:05 PM, Afsane Farhadi wrote: what do I have to do for solving this mater? I want to use a opls as forcefield. how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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] potential energy doesn't have negative value
On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
[gmx-users] potential energy doesn't have negative value
I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. Sent from Yahoo Mail on Android-- 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.
