Re: [gmx-users] Fwd: charges,resonance and electrostatics
Omer Markovitch wrote: There is no non-bonded interaction between these two oxygens, unless you are using an Urey-Bradley potential for the angle, like in the CHARMM force field. Most (if not all) of the standard force fields in Gromacs treat the interaction of these oxygens within an angle definition, which is a bonded term. -Justin So no coloumb law between the two oxygens? 10x, Omer. Right, 1-3 interactions are accounted for within bonded (angle) definitions, unless you are applying an Urey-Bradley potential. -Justin ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] Fwd: charges,resonance and electrostatics
> > >> There is no non-bonded interaction between these two oxygens, unless you >> are using an Urey-Bradley potential for the angle, like in the CHARMM force >> field. Most (if not all) of the standard force fields in Gromacs treat the >> interaction of these oxygens within an angle definition, which is a bonded >> term. >> >> -Justin > > So no coloumb law between the two oxygens? 10x, Omer. ___ 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] Fwd: charges,resonance and electrostatics
Omer Markovitch wrote: Hello, There is a point, I want to clear out for myself: Say we focus on the aspartate residue. It has a formal charge of -1. This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2), according to one of the force fields employed in GROMACS. What is the right way to calculate electrostatics here: 1) "As is", and letting the two oxygens repel one another. 2) Ignore this specific pair when calculating? How does GROMACS operates? I think that (1) is the common practice, but I want to be sure. There is no non-bonded interaction between these two oxygens, unless you are using an Urey-Bradley potential for the angle, like in the CHARMM force field. Most (if not all) of the standard force fields in Gromacs treat the interaction of these oxygens within an angle definition, which is a bonded term. -Justin Thank you, Omer Markovitch. (this email was sent to gmx-dev. by mistake) Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] Fwd: charges,resonance and electrostatics
Hello, There is a point, I want to clear out for myself: Say we focus on the aspartate residue. It has a formal charge of -1. This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2), according to one of the force fields employed in GROMACS. What is the right way to calculate electrostatics here: 1) "As is", and letting the two oxygens repel one another. 2) Ignore this specific pair when calculating? How does GROMACS operates? I think that (1) is the common practice, but I want to be sure. Thank you, Omer Markovitch. (this email was sent to gmx-dev. by mistake) Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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
