Good day, I have generated npt.tpr for my protein ligand and changed my npt.mdp file according to the suggestions by GROMACS for using Brendsen and h-bonds for constraints finally I encounter this NOTE which I think will cause further problems in my md run : NOTE 1 [file topol.top, line 18260]: The bond in molecule-type UNL between atoms 6 C5 and 7 C6 has an estimated oscillational period of 1.8e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group Protein_UNL is 4960.82 Number of degrees of freedom in T-Coupling group Water_and_ions is 77850.18 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm I would appreciate it if someone tells me what I need to do with my system I think it may be related to the time step of my simulaiton and frames as I searched the similar issues. thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- 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.
