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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The dielectric constant of your water model will not be 80,<br>it depends on the water model.<br>But when you have many ions, the effective dielectric constant<br>of the water will be lower.<br><br>Your mdp parameters are very non-standard.<br>You should not use a cut-off of 0.7 nm with a grid spacing of 0.12.<br>I would suggest to use a cut-off of 0.9 nm.<br><br>For efficiency you would want to have a time step of 2 fs<br>and grid search instead of neighbor search.<br><br>Or have you done all this because your box is very small?<br>For such charged systems you need a relatively large box.<br></div><br>Berk<br><br><hr id="stopSpelling">> Date: Wed, 13 Aug 2008 22:48:59 +0530<br>> From: avinashk.iit.kgp@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Dielectric constant<br>> <br>> Dear users,<br>> <br>> I am trying to simulate electroosmotic flow using GROMACS.<br>> The liquid is water and I am trying to find the dielectric constant of<br>> water. I am just getting a value of dielectric constant of 10. i am<br>> expecting 80 for water. I am attaching my mdp . I would be grateful if<br>> somebody points some mistake.<br>> <br>> title = md<br>> cpp = cpp<br>> include = -I../top<br>> define =<br>> <br>> <br>> integrator = md<br>> tinit = 0<br>> dt = 0.001<br>> nsteps = 700000<br>> init_step = 0<br>> comm-mode = Linear<br>> nstcomm = 500<br>> comm-grps =<br>> bd-fric = 0<br>> ld-seed = 1993<br>> emtol = 10<br>> emstep = 0.01<br>> niter = 20<br>> fcstep = 0<br>> nstcgsteep = 1000<br>> nbfgscorr = 10<br>> nstxout = 100<br>> nstvout = 100<br>> nstfout = 100<br>> nstcheckpoint = 20<br>> nstlog = 100<br>> nstenergy = 10<br>> nstxtcout = 0<br>> xtc-precision = 1000<br>> xtc-grps =<br>> energygrps = WA WA1 WA2 SOL NA+<br>> nstlist = 10<br>> ns_type = simple<br>> pbc = xyz<br>> rlist = 0.7<br>> domain-decomposition = no<br>> coulombtype = PME<br>> rcoulomb-switch = 0<br>> rcoulomb = 0.7<br>> epsilon_r = 1<br>> epsilon_rf = 1<br>> vdw-type = Cut-off<br>> rvdw-switch = 0<br>> rvdw = 0.7<br>> DispCorr = No<br>> table-extension = 1<br>> energygrp_table =<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4<br>> ewald_rtol = 1e-05<br>> ewald_geometry = 3dc<br>> epsilon_surface = 0<br>> optimize_fft = no<br>> <br>> gb_algorithm = Still<br>> nstgbradii = 1<br>> rgbradii = 2<br>> gb_saltconc = 0<br>> <br>> implicit_solvent = No<br>> <br>> tcoupl = Berendsen<br>> tc-grps = WA WA1 WA2 SOL NA+<br>> tau_t = 0.1 0.1 0.1 0.1 0.1<br>> ref_t = 300 300 300 300 300<br>> Pcoupl = No<br>> Pcoupltype = Isotropic<br>> tau-p = 1<br>> compressibility =<br>> ref-p =<br>> andersen_seed = 81513<br>> constraints = all-bonds<br>> constraint-algorithm = Lincs<br>> unconstrained-start = no<br>> Shake-SOR = no<br>> shake-tol = 1e-04<br>> lincs-order = 4<br>> lincs-iter = 1<br>> lincs-warnangle = 30<br>> morse = no<br>> <br>> ; ENERGY GROUP EXCLUSIONS<br>> ; Pairs of energy groups for which all non-bonded interactions are excluded<br>> energygrp_excl =<br>> <br>> <br>> disre = No<br>> <br>> disre-weighting = Conservative<br>> <br>> disre-mixed = no<br>> disre-fc = 1000<br>> disre-tau = 0<br>> <br>> nstdisreout = 100<br>> <br>> orire = no<br>> <br>> orire-fc = 0<br>> orire-tau = 0<br>> orire-fitgrp =<br>> <br>> nstorireout = 100<br>> <br>> dihre = No<br>> dihre-fc = 1000<br>> dihre-tau = 0<br>> <br>> nstdihreout = 100<br>> <br>> ; Free energy control stuff<br>> free-energy = no<br>> init-lambda = 0<br>> delta-lambda = 0<br>> sc-alpha = 0<br>> sc-power = 1<br>> sc-sigma = 0.3<br>> <br>> ; Non-equilibrium MD stuff<br>> acc-grps =<br>> accelerate =<br>> freezegrps = WA WA1 WA2<br>> freezedim = y y y y y y y y y<br>> cos-acceleration = 0<br>> deform =<br>> <br>> ; Electric fields<br>> ; Format is number of terms (int) and for all terms an amplitude (real)<br>> ; and a phase angle (real)<br>> E_x = 1 0.1 0<br>> E-xt =<br>> E-y =<br>> E-yt =<br>> E-z =<br>> E-zt =<br>> <br>> <br>> <br>> <br>> -- <br>> Avinash Kumar.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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