On 10/3/19 10:27 PM, Adip Jhaveri wrote:
Hello all, I am simulating a system of two proteins in solution. For the simulation I has specified (in the .mdp file) energygrps as : Protein W_ION. Now in the output energy file, these energy groups are separated only for the Columbic and LJ interactions: For e.g. (Columbic : Protein-Protein), (Columbic Protein - W_ION). Is it possible to get a similar decomposition for the bonded energy terms? (Like Bond: Protein, G96Angle: Protein)
energygrps decompose short-range nonbonded terms, so no. The only way to get such terms is to make a .tpr containing only the species of interest and a corresponding .xtc/.trr and use mdrun -rerun to get the energies.
Also, is it possible during post-processing to get energies for a different group like for each individual protein (e.g Protein_A) or would I have to run the simulation again with different energy groups?
Use mdrun -rerun as stated above. -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.
