Dear Gromacs Users, I'm trying to embed a protein into a lipid bilayer using the -membed option of gmx mdrun. After executing the command: gmx mdrun -s topol.tpr -deffnm out -membed embed.dat -mp topol.top -mn index.ndx I select the groups for the Protein and Lipid_Bilayer when prompted for them, and then I get an error message:
Program: gmx mdrun, version 2016 Source file: src/gromacs/topology/mtop_util.cpp (line 249) Software inconsistency error: gmx_mtop_atomlookup_settle_init called without settles I have tried searching online via Google for the meaning and solution to this error, but all I can find are links to the source code that contains that method call. Section 6.14 of the Gromacs User Manual doesn't contain any information to address this error. Additionally this error isn't listed at www.gromacs.org/Documentation/Errors. I have tried this with and without the -mp and -mn options, and I receive the same response. I have checked all of the input files (system.gro, index.ndx, topol.top, embed.mdp, & embed.dat) for errors, and everything looks correct. Before executing mdrun I run gmx grompp and it completes without any warnings or errors. It produces a few common notes, which I consider to be okay and not relevant to this error. Here is a subset of the mdp parameters which could potentially be relevant: comm-mode = Linear comm-grps = System cutoff-scheme = group ; Verlet is not yet implemented for use with membed tcouple = v-rescale tc-groups = Protein Lipid_Bilayer Water Pcoupl = no freezegrps = Protein freezedim = Y Y Y energygrps = Protein energygrp_excl = Protein Protein I am using the Martini 2.2 coarse grain force field. I have used this force field for other md simulations without using the membed tool, and this error was never produced. Can anyone offer any guidance or pointers about what I could be doing wrong or otherwise a way work around the error? Thank you for reading, Jason -- 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 [email protected].
