Hi Justin,
Thank you very much for your suggestions, I ran the equilibration! After running the equilibration, I tabulated the temperature with time, and at time=0 the temperature is 277.73 K and at time=1ps the temperature is 294.03. The initial temperature is enough similar (I think) to the considered one. However, the temperature at 1ps is lower than the stated one (298K) in the annealing settings (and therefore at 0.134 ps the temperature is lower than 294 K instead of 298K). I copy the .mdp file in case you can detect the errors in this file, as I have been looking for the annealing settings in the GROMACS manual and in previous posts and I don't find what is wrong. title = Lipid NVT equilibration define = -DPOSRES ; position restrain the lipid ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 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 = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme vdwtype = Cut-off vdw_modifier = Potential-shift-Verlet 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 coulomb_modifier = Potential-shift-Verlet ; 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 = 278 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ;Simulated annealing annealing = single annealing_npoints = 2 annealing_time = 0 0.134 annealing_temp = 278 298 If I have understood correctly from previous posts, gen_temp must be equal to the lower annealing temperature (in this case 278K) and the ref_t must be equal to the highest annealing temperature (in this case 298 K), is it correct? Thak you for all your help, 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: jueves, 20 de septiembre de 2018 16:45:21 Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Error in NVT equilibration On 9/19/18 6:14 AM, Gonzalez Fernandez, Cristina wrote: > Hi Justin, > > > I’ve been looking for the non-bonded setting parameters for the GROMOS force > field. I have found that for this force field coulmb_modifier and > vdw_modifier = Potential-shift-Verlet. I have changed this in the .mdp file, > but I don’t have seen more differences, Is it correct? Is it enough to change > the columb and vdw modifier option?. I obtain the same error when running the > equilibration. I haven't used the GROMOS force fields with the new Verlet options, and it was parametrized for rather old algorithms, so I can't offer you the latest advice on this. Electrostatic forces are typically computed with PME, and a plain cutoff for vdW. Your cutoff values in the previous .mdp file were also incorrect and need to be fixed; it's not just a matter of the modifiers. > > I have tryied to use the default GMX values for dt (0,002) and nsteps (50000) > because they are so different to the ones I have proposed (0,015 and 6667 > respectively) and the nvt equilibration runs. My values derive from the A time step of 15 fs is not going to be stable with an atomistic force field. A sensible dt is usually no larger than 2 fs without playing other tricks. > annealing I am trying, and with the default values the annealing is not > fulfilled since the temperature doesn’t start in the first annealing > temperature. > > > I need to increase the temperature from 278 to 298K with a rate of 0,298 K > every time step for 1 ps. I checked your previous posts and use annealing for > that purpose. From the rate 0,298K/step and knowing that I need to increase > 20 K de temperature, I calculate the requied number of steps and from this > value and 1 ps I found that dt should be 0,015 ps. From this dt, as I > considered a total equilibration time of 100 ps, I calculated nsteps (6667). Don't adjust dt, which is the simulation time step. Your simulation will never be stable with such a value. You can't simultaneously specify a heating rate, total change, and fixed time interval. You should consider dt fixed and determine how much time it will take to reach the total change in temperature at the desired rate. For your situation, to heat by 20 K with a rate of 0.298 K/2fs, you would need to warm over a period of about 134 ps. > > The annealing settings are: > > ;Simulated annealing > > annealing = single > > annealing_npoints = 2 > > annealing_time = 0 1 > > annealing_temp = 278 298 > > How can I satisfy the 0,298K increase during 1 ps until 298K while running > the equilibration? Change annealing_time = 0 134 and you'll get the rate of heating that you want. As stated above, you can't do it in 1 fs while also specifying the rate of heating. dt is not a dependent variable that is subject to such manipulations. -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? 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