Hi,
As I am using the GROMOS froce field, I constrained all bonds as suggested. However, I obtained the same error. I copy the .mdp file in case there are errors and you can help me to find them: title = Lipid NVT equilibration define = -DPOSRES ; position restrain the Lipid ; Run parameters integrator = md ; leap-frog integrator nsteps = 6667 ; 2 * 50000 = 100 ps dt = 0.015 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; bonds involving H are constrained ;shake_tol = 0.0001 lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rlist = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme vdwtype = Cut-off vdw_modifier = Force-switch rvdw_switch = 1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ewald-rtol = 1e-6 pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 298 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ;Simulated annealing annealing = single annealing_npoints = 2 annealing_time = 0 1 annealing_temp = 278 298 Thank you in advance, C. ________________________________ De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin Lemkul <jalem...@vt.edu> Enviado: lunes, 17 de septiembre de 2018 14:06:24 Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Error in NVT equilibration On 9/17/18 8:04 AM, Vytautas Rakeviius wrote: > 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. That depends on the force field convention. It is not universally appropriate to constrain all bonds (and certainly should not be the "solution" to just "make the warning go away"), and the warning from grompp may not actually be the source of any problem. -Justin > 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. -- ================================================== 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. -- 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.