I am using PME, can you elaborate about the decomposing you mentioned? ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, April 03, 2013 2:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 1-4 interactions
On 4/3/13 7:16 AM, Liron Cohen wrote: > After reading the manual and trying to find more information on the mailing > list. I'm still not sure about this 1-4 interactions, when I want to > calculate the energy between two groups (lets say one residue and the rest of > the protein) should I sum everything (including the 1-4 interactions) or > should I only include the SR interactions. 1-4 interactions are intramolecular and thus should not be included in intermolecular energies. If you're using PME, decomposing the long-range component to the electrostatics term is challenging. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 list gmx-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 list gmx-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
