Hi, On Tue, Dec 3, 2019 at 7:37 AM Mijiddorj B <b.mijidd...@gmail.com> wrote:
> Dear GMX users, > Hello, I would like to discuss the grompp message that tells the bonded > atoms oscillational period less than 10 times the time step. I am using > 0.002 ps time step. The choice of the time step depends on the force field parameter set. and bond oscillation of light atoms (e.i H) determines the time step. I suggest to follow the indication given by the developers of the force field you are using. The simulation was stopped because of LINCS warming. > > Pls note that constraints can be applied to a) only bond containing H b) to all bonds (but and also to angle and so on). Best regards Alessandra > Is it need to decrease time step at least 10 times? > > Instead of this, can I remove constraint and use the 0.0005 ps time step? > > On the other hand, after long equilibration with 0.0001 time step, can I > increase the time step until 0.001? > > How can I solve this problem? > If you have any experience, please let me advice. Thank you. > > Regards, > Mijiddorj > -- > 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.