Thanks for the help Flo, At step 3 are you running NPT? Out of interest do you have any water in the box? If so which model are you using for the water?
Laura ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Florian Dommert [domm...@icp.uni-stuttgart.de] Sent: 14 May 2013 10:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] setting up a simulation of an ionic liquid Hi, perhaps try for the first 1000-100000 steps to set nstlist=1. I also had very much trouble with setting up IL systems, but now I have the following routine: 1. use genbox to fit the cations and anions in a large box 2. energy minimization 3. run with nstlist=1, perhaps even particle decomposition is required until a reasonable density is achieved 4. equilibrated with nstlist=10 or even larger After 500-1000ps I usually get an system with converged density, which I finally equilibrated for further 5-10ns. Cheers, Flo * Laura Leay <laura.l...@postgrad.manchester.ac.uk> [2013-05-14 09:13:55 +0000]: >Thanks for the help Justin, > >I've taken a look at the atom with the maximum force using VMD and I can't see >anything wrong with it. Its part of a whole molecule and not particularly >close to any other molecules either. I suspect I may need to take another look >at the force field but want to make sure there is nothing in my mdp file that >could be causing problems. I've no experience of simulating ionic liquids and >from what I've read it can be quite tricky. > >The paper I'm using for the nitric is J Phys Chem B, 2001, 105(45), 11131. >Here they use a twin range cut off of 12/15 A. The papers for the other >molecules I'll eventually be adding to the simulation use a cut off of 15 A so >this seemed the most sensible option. Is there anything else you would suggest? > >Any help is greatly appreciated. > > >________________________________________ >From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf >of Justin Lemkul [jalem...@vt.edu] >Sent: 13 May 2013 23:05 >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] setting up a simulation of an ionic liquid > >On 5/13/13 11:50 AM, Laura Leay wrote: >> All, >> >> I've seen a few threads about simulations in ionic liquds but have not come >> across anything that tells me what settings I should use in my mdp file. The >> system is nitric acid which has fully dissociated into NO3- and HO3+. The >> simulation will run fine with just the ions at low density under NVT. >> However, when I solvate the box with SPC water (using the Amber force field) >> the simulation energy minimises with a really maximum force, of the order of >> 10^5. If I try to run an NPT simulation it immediately crashes and the >> md.log fle reveals that the electrostatic potential was unreasonable high, >> resulting in NaN. >> > >You should investigate which atom bears the maximum force; that will point to >the source of your problem. > >> Below is the mdp file I've been using. I've been using PME electrostatics. >> If anyone can suggest some changes to make I would appreciate it. >> > >The force field dictates most of the settings, most notably the cutoff. The >value of rvdw seems wrong, at least. > >-Justin > >> Laura >> >> PS, Justin, you were right earlier, there was a problem with my toplogy >> causing renaming of residues, I just hadn't spotted it. Thanks for your >> reply. >> >> ------------- >> >> >> ; VARIOUS PREPROCESSING OPTIONS >> title = Yo >> cpp = /usr/bin/cpp >> include = >> ;define = -DFLEXIBLE >> >> ; RUN CONTROL PARAMETERS >> integrator = steep ;md for simulation, steep for Emin >> ; Start time and timestep in ps >> tinit = 0 >> dt = 0.0001 >> nsteps = 50000000 ;remove 3 >> ; For exact run continuation or redoing part of a run >> init_step = 0 >> ; mode for center of mass motion removal >> comm-mode = Linear >> ; number of steps for center of mass motion removal >> nstcomm = 1 >> ; group(s) for center of mass motion removal >> comm-grps = >> >> ; LANGEVIN DYNAMICS OPTIONS >> ; Temperature, friction coefficient (amu/ps) and random seed >> ;bd-temp = 300 >> bd-fric = 0 >> ld-seed = 1993 >> >> ; ENERGY MINIMIZATION OPTIONS >> ; Force tolerance and initial step-size >> emtol = 100 >> emstep = 0.01 >> ; Max number of iterations in relax_shells >> niter = 20 >> ; Step size (1/ps^2) for minimization of flexible constraints >> fcstep = 0 >> ; Frequency of steepest descents steps when doing CG >> nstcgsteep = 1000 >> nbfgscorr = 10 >> >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> ; Checkpointing helps you continue after crashes >> nstcheckpoint = 1000 >> ; Output frequency for energies to log file and energy file >> nstlog = 50 >> nstenergy = 50 >> ; Output frequency and precision for xtc file >> nstxtcout = 50 >> xtc-precision = 1000 >> ; This selects the subset of atoms for the xtc file. You can >> ; select multiple groups. By default all atoms will be written. >> xtc-grps = >> ; Selection of energy groups >> energygrps = >> >> ; NEIGHBORSEARCHING PARAMETERS >> ; nblist update frequency >> nstlist = 10 >> ; ns algorithm (simple or grid) >> ns_type = grid >> ; Periodic boundary conditions: xyz (default), no (vacuum) >> ; or full (infinite systems only) >> pbc = xyz >> ; nblist cut-off >> rlist = 0.9 >> domain-decomposition = no >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 0.9 >> ; Dielectric constant (DC) for cut-off or DC of reaction field >> epsilon-r = 1 >> ; Method for doing Van der Waals >> vdw-type = Cut-off >> ; cut-off lengths >> rvdw-switch = 0 >> rvdw = 1.5 >> ; Apply long range dispersion corrections for Energy and Pressure >> DispCorr = EnerPres >> ; Extension of the potential lookup tables beyond the cut-off >> table-extension = 1 >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters >> pme_order = 4 >> ewald_rtol = 1e-05 >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = no >> >> ; GENERALIZED BORN ELECTROSTATICS >> ; Algorithm for calculating Born radii >> gb_algorithm = Still >> ; Frequency of calculating the Born radii inside rlist >> nstgbradii = 1 >> ; Cutoff for Born radii calculation; the contribution from atoms >> ; between rlist and rgbradii is updated every nstlist steps >> rgbradii = 2 >> ; Salt concentration in M for Generalized Born models >> gb_saltconc = 0 >> >> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) >> implicit_solvent = No >> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS >> ; Temperature coupling >> Tcoupl = berendsen >> ; Groups to couple separately >> tc-grps = System >> ; Time constant (ps) and reference temperature (K) >> tau_t = 0.1 >> ref_t = 300 >> ; Pressure coupling >> Pcoupl = berendsen >> Pcoupltype = semiisotropic >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) >> tau_p = 1.0 >> compressibility = 0 4.5e-5 >> ref_p = 1.0 1.0 >> ; Random seed for Andersen thermostat >> andersen_seed = 815131 >> >> ; SIMULATED ANNEALING >> ; Type of annealing for each temperature group (no/single/periodic) >> annealing = no >> ; Number of time points to use for specifying annealing in each group >> annealing_npoints = >> ; List of times at the annealing points for each group >> annealing_time = >> ; Temp. at each annealing point, for each group. >> annealing_temp = >> >> ; GENERATE VELOCITIES FOR STARTUP RUN >> gen_vel = yes >> gen_temp = 300 >> gen_seed = 1993 >> >> ; OPTIONS FOR BONDS >> ;constraints = all-bonds >> ; Type of constraint algorithm >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration >> unconstrained-start = no >> ; Use successive overrelaxation to reduce the number of shake iterations >> Shake-SOR = no >> ; Relative tolerance of shake >> shake-tol = 1e-04 >> ; Highest order in the expansion of the constraint coupling matrix >> lincs-order = 4 >> ; Number of iterations in the final step of LINCS. 1 is fine for >> ; normal simulations, but use 2 to conserve energy in NVE runs. >> ; For energy minimization with constraints it should be 4 to 8. >> lincs-iter = 1 >> ; Lincs will write a warning to the stderr if in one step a bond >> ; rotates over more degrees than >> lincs-warnangle = 30 >> ; Convert harmonic bonds to morse potentials >> morse = no >> >> ; ENERGY GROUP EXCLUSIONS >> ; Pairs of energy groups for which all non-bonded interactions are excluded >> energygrp_excl = >> >> > >-- >======================================== > >Justin A. Lemkul, Ph.D. >Research Scientist >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr.rer.nat. Florian Dommert Institute for Computational Physics University Stuttgart Allmandring 3 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
