Yes, I am running NpT with Berendsen coupling. So far I have just dealt with neat ILs, so I have no experience with water. But as Justin mentioned, do not change the parameters given by the FF, which can really introduce strange artefacts, e.g too high or too low density, dynamics, ...
Cheers, Flo * Laura Leay <laura.l...@postgrad.manchester.ac.uk> [2013-05-14 10:39:00 +0000]:
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. -JustinLaura 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
-- 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
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