Re:Re: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.
Dear Justin, Thank you so much for your help! Best wishes Fugui At 2013-07-28 03:52:47,"Justin Lemkul" wrote: > > >On 7/27/13 11:48 AM, xiao wrote: >> Dear Gromacs users, >> >> I am developing the force field parameters of an organic molecule. I need to >> calculate the MM energy of the molecule in a fixed conformation. For >> example, in order to get the force constant of a bond, i need to calculate >> the energy of the bond in different distance by using MM method and the QM >> method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from >> the equilibrium value at a step size of 0.005 angstrom while optimizing the >> structure at each step by using QM method. Secondly, i calculate the >> potential energy of each structure obtained in the previous QM optimizaiton >> step. Thirdly, i will calculate the energy difference between QM and MM >> calculation, and finally fit the force constant of the bond using the energy >> difference between QM and MM energy. My question is that how i calculate >> the potential energy of each structure obtained in QM step? I think i can >> get an potential energy in energy minization step by using grompp method, >> but i am not sure whe ! > the >> r it is the energy i needed. Any advice is appreciated. >> > >http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 601 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >== >-- >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 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: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.
On 7/27/13 11:48 AM, xiao wrote: Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using MM method and the QM method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value at a step size of 0.005 angstrom while optimizing the structure at each step by using QM method. Secondly, i calculate the potential energy of each structure obtained in the previous QM optimizaiton step. Thirdly, i will calculate the energy difference between QM and MM calculation, and finally fit the force constant of the bond using the energy difference between QM and MM energy. My question is that how i calculate the potential energy of each structure obtained in QM step? I think i can get an potential energy in energy minization step by using grompp method, but i am not sure whe! the r it is the energy i needed. Any advice is appreciated. http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] How to calculate the potential energy of a molecule in a fixed conformation.
Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using MM method and the QM method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value at a step size of 0.005 angstrom while optimizing the structure at each step by using QM method. Secondly, i calculate the potential energy of each structure obtained in the previous QM optimizaiton step. Thirdly, i will calculate the energy difference between QM and MM calculation, and finally fit the force constant of the bond using the energy difference between QM and MM energy. My question is that how i calculate the potential energy of each structure obtained in QM step? I think i can get an potential energy in energy minization step by using grompp method, but i am not sure whethe r it is the energy i needed. Any advice is appreciated. Best wishes Fugui -- 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
