I think your attachment to email was lost during re-transfer and it would be nice to see that, but I think what you need is:constraints = all-bondsIn that mdp file.
On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, Cristina <cristina.gonzalezf...@unican.es> wrote: Dear Gromacs users, I am trying to perform a nvt equilibration, but when I generate the .tpr file I get a warning indicating that a bond is oscillating too fast: The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an estimated oscillational period of 2.4e-02 ps, which is less than 5 times the time step of 1.5e-02. Maybe you forgot to change the constraints mdp option. I have ignored it with the -maxwarn option and I obtain the .tpr file. However, when I run the simulation I obtain this error? Too many LINCS warnings (1630) Are the error and the warning related? How could I solve the Lincs error and the warning? I attach the .mdp file. Thank you in advance, C. -- 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.