Hello! I performed simulations with the small molecules in water and faced with the fact that in about 5% of cases, the simulation falls at the last step with an error:
------------------------------------------------------- Program: gmx mdrun, version 2018.4 Source file: src/gromacs/pbcutil/mshift.cpp (line 906) Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 47 atoms. The longest distance involved in such interactions is 1.298 nm which is close to half the box length. This molecule type consists of multiple parts, e.g. monomers, that are connected by interactions that are not chemical bonds, e.g. restraints. Such systems can not be treated. The only solution is increasing the box size. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- The problem occurs when simulating in a rhombic dodecahedron cell with the standard distance between solute and the box 1nm. There is no such error in the cubic cell with distance 1nm. Trying to establish the reason for this behavior, I found that it is associated with the presence of virtual atoms in a small molecule. When I exchange a virtual atom for an atom linked by a chemical bond to the rest of the molecule, an error does not appear. I want to remove errors while preserving virtual atoms as well as the size and shape of the cell. Maybe someone already encountered this behavior and knows what my mistake is. I will be glad of any help. The link https://drive.google.com/file/d/0B5NzD-LVrUalbDdSblhfTkowUDN1aWxER3hlLWhaRFROcjhj/view?usp=sharing contains files for 1-step molecular dynamics that failed with my system of interest. Gromacs version - 2018.4. Thank you, Artem Shekhovtsov -- 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.