On 2/17/20 7:18 AM, Peter Mawanga wrote:
Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. Hence I am not able to calculate the energy between the protein and ligand using the energy (.edr) file. Please let me know if there is any workaround for this. It would be difficult to repeat the simulations again.
Computing interaction energy is a post-processing task. You should not specify energygrps in your .mdp file for the actual simulation because (1) it slows the simulation down and (2) it's not compatible with GPUs.
All you need to do is generate a new .tpr file with the desired energygrps (you don't even need a special index file because all non-standard [moleculetype] entries are by default assigned to their own index groups) and use mdrun -rerun on the existing trajectory and the new .tpr file with energygrps.
-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.
