when i try to run mdrun they start showing this: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom= 2881 Step= 1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom= 2881 Step= 2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom= 2881 Step= 3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom= 2881 Step= 4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom= 2881 Step= 5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom= 2881 Step= 6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom= 2881 Step= 7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom= 2881 Step= 8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom= 2881 Step= 9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom= 2881 Step= 10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom= 2881 Step= 11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom= 2883 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom= 2903 Step= 13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom= 2883 Step= 14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom= 2883 Step= 15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom= 2881
step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) I don't understand what happend. Please can you help me? How i can reduce timestep? Em ter, 18 de set de 2018 às 08:36, Justin Lemkul <jalem...@vt.edu> escreveu: > > > On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: > > These were the errors until the moment of executing the minimization: > > > > After adding ions grompp: > > NOTE 1 [file topol.top, line 37566]: > > System has non-zero total charge: -18.999999 > > Total charge should normally be an integer. See > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > for discussion on how close it should be to an integer. > > > > minimization mdrun > > step 16: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > tMPI error: Receive buffer size too small for transmission (in valid > comm) > > Abort (core dumped) > > > > In attach send you the mdp archive for minimization run. > > The mailing list does not allow attachments. > > Use the -v flag of mdrun to track the energy and forces at every step > until the crash to see what's going on and where the maximum force is > acting. There's probably a bad contact somewhere that can't be relaxed > and you need to investigate why that's happening. > > -Justin > > > Thanks for your help > > > > Em seg, 17 de set de 2018 às 19:56, Justin Lemkul <jalem...@vt.edu> > > escreveu: > > > >> > >> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > >>> Hi everyone. > >>> I'm trying simulate a protein in water followin lysozyme tutorial using > >>> gromacs 2016.3. When triying minimize the system after make the box and > >>> insert a salt concentration the minimization has been stoped sendingme > >> the > >>> following error: > >>> > >>> step 16: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> Wrote pdb files with previous and current coordinates > >>> tMPI error: Receive buffer size too small for transmission (in valid > >> comm) > >>> Abort (core dumped) > >> Water SETTLE problems are not unusual in energy minimization and are > >> often resolved. If, however, such a message immediately precedes a > >> failure, then you have a serious problem with either the coordinates or > >> topology. mdrun prints out which atom is experiencing the maximum force, > >> so start by looking there, as well as reviewing your notes about what > >> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have > >> ignored any, right? :). > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > >> > > > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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.