I am fairly new to gromacs and I am trying to run a thermodynamic integration simulation of a ligand disappearing in a box of octanol at a single set lambda point. I have previous successful nvt and npt runs of this system. When I have added the free energy portions to the input file, I get the following error:
Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This seems unusual. The box dimensions are 9.45 nm x 9.45 x 9.45 nm so that is fairly large even accounting for some shrinkage with a disappearing ligand. Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2, rcoulomb=1.2. Doubling any of them would still be less than 3 nm which is significantly smaller than the box size. Is there anything I am missing or any suggestions that others can give me? Thank you, Scott -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
