Hi, > On 14 Mar 2017, at 11:18, Vries, de, H.W. <h.w.de.vrie...@student.rug.nl> > wrote: > > 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. How does your topol.top file look like? It should list the correct number of copies of each ion / molecule.
Is this the most recent version (2016)? Best, Carsten > > 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. -- 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.