Re: [gmx-users] bonded interactions in Gromos96
On 10/11/13 1:31 PM, Ehsan Sadeghi wrote: Thanks Justin. Do you know how can I find these coefficients for the atom interactions which are not defined in Gromos? I have (-(CF2CF2)4 -)(-O-CF2CF(CF3 )-O-CF2 CF2-SO3H) molecule. I need C-F, C-S, C-S-O interactions. Can I use predefined ones? which one? Bond lengths typically come from crystallography and force constants from spectroscopy. If they don't already exist in the parent force field and no one has derived them in subsequent work, you're stuck deriving them yourself based on whatever experimental evidence is available. -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
Re: [gmx-users] bonded interactions in Gromos96
Thanks Justin. Do you know how can I find these coefficients for the atom interactions which are not defined in Gromos? I have (-(CF2CF2)4 -)(-O-CF2CF(CF3 )-O-CF2 CF2-SO3H) molecule. I need C-F, C-S, C-S-O interactions. Can I use predefined ones? which one? All the best, Ehsan - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Friday, October 11, 2013 9:44:33 AM Subject: Re: [gmx-users] bonded interactions in Gromos96 On 10/11/13 12:40 PM, Ehsan Sadeghi wrote: > Hi gromacs users, > > I tried to add new bonded interactions to the ffbonded.itp file in gromos96, > but I am confused about the used parameters in the descriptions. Here is an > example: > > #define gb_10.1000 1.5700e+07 > ; H - OA 750 > > The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 > > I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: > 0.1000, 1.5700e+07, 750. > > > The same story for the angle potential: > > #define ga_1 90.00 380.00 > ; NR(heme) - FE - C 90 > > > The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - > cos(theta0_ijk))^2 > > I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the > definition: 90.00, 380, 90. > The numbers in the comment lines are bond indices from the Gromos96 force field files. They are irrelevant. -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] bonded interactions in Gromos96
On 10/11/13 12:40 PM, Ehsan Sadeghi wrote: Hi gromacs users, I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example: #define gb_10.1000 1.5700e+07 ; H - OA 750 The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750. The same story for the angle potential: #define ga_1 90.00 380.00 ; NR(heme) - FE - C 90 The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2 I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90. The numbers in the comment lines are bond indices from the Gromos96 force field files. They are irrelevant. -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] bonded interactions in Gromos96
Hi gromacs users, I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example: #define gb_10.1000 1.5700e+07 ; H - OA 750 The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750. The same story for the angle potential: #define ga_1 90.00 380.00 ; NR(heme) - FE - C 90 The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2 I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90. I appreciate if somebody could clarify this for me. Ehsan -- 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
