Dear all, I am currently trying to run the computational electrophysiology scheme on an implicit solvent, coarse-grained system by introducing a little workaround:
In the manual, it is stated that we can tell the routine what molecules are 'solvent', and what molecules are 'ions' through custom index groups. As my system thus does not have water molecules, I inserted non-interacting dummy particles into the system, which I then tell the CompEl scheme to use as a solvent group for swapping (via custom index groups) However, the simulation gets stuck at: SWAP: Making sure each atom belongs to at most one of the swap groups. SWAP: Checking whether all ion molecules consist of 20012 atoms SWAP: Checking whether all solvent molecules consist of 20012 atoms SWAP: Opening output file swapions.xvg SWAP: Determining initial ion counts. Looking at swapions.xvg, I see that the routine doesn't recognize my coarse-grained atoms correctly: 4800,7206 and 800 are the correct numbers of coarse-grained atoms that I put in, with 20012 being the total number of coarse-grained beads that I have in my system: # ion group contains 4800 atoms with 20012 atoms in each molecule. # split0 group contains 7206 atoms. # split1 group contains 7206 atoms. # solvent group contains 800 atoms with 20012 atoms in each molecule. Can anyone give me a pointer as to what might be going wrong (I can send the files directly if requested)? Could this be an issue with the coarse-grained model im employing, that it is not defined properly in my topology, or is CompEl really incompatible with any implicit solvent CG-representation that tries to use dummy particles for swapping purposes? Thank you kindly, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience Micromechanics of Materials Group tel: +31 (0)6-30520328 office: X5113.0129 Nijenborgh 4, 9747AG Groningen, Netherlands -- 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.