<div>
        <p>
                Dear sir£º</p>
        <p>
                 </p>
        <p>
                Thank you for reading my letter. </p>
        <p>
                I have a few problems in Shell MD<br />
                <br />
                <span style="display: none"> .... .</span> I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help.</p>
        <p>
                 And this is my own *.mdp file below<br />
                <br />
                 </p>
        <p>
                <span style="font-size: 14px"><em><strong>include =<br />
                define =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>integrator = sd<br />
                tinit = 0<br />
                dt = 0.004<br />
                nsteps = 10000000<br />
                simulation_part = 1<br />
                init_step = 0<br />
                comm-mode nstcomm = Linear<br />
                 = 100<br />
                comm-grps = System</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>bd-fric = 1<br />
                ld-seed = 1993</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>emtol = 10<br />
                emstep = 0.01<br />
                niter = 20<br />
                fcstep = 0<br />
                nstcgsteep = 1000<br />
                nbfgscorr = 10</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>rtpi = 0.05</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>nstxout = 1000000<br />
                nstvout = 1000000<br />
                nstfout = 1000000<br />
                nstlog = 10<br />
                nstenergy = 10<br />
                nstxtcout = 10<br />
                xtc_precision = 10<br />
                xtc-grps =<br />
                energygrps = CR1</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>nstlist = 1<br />
                ns_type = grid<br />
                pbc = xyz<br />
                periodic_molecules = no <br />
                rlist = 2.0</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>coulombtype = User<br />
                rcoulomb_switch = 0.0<br />
                rcoulomb = 2.0<br />
                epsilon_r = 1<br />
                epsilon_rf = 1<br />
                vdw_type = User<br />
                rvdw_switch = 0.0<br />
                rvdw = 2.0<br />
                DispCorr = No<br />
                table_extension = 0<br />
                energygrp_table = CR1 CR1<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 = 3d<br />
                epsilon_surface = 0<br />
                optimize_fft = yes</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>implicit_solvent = No</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>gb_algorithm = Still<br />
                nstgbradii = 1<br />
                rgbradii = 2<br />
                gb_epsilon_solvent = 80<br />
                gb_saltconc = 0<br />
                gb_obc_alpha = 1<br />
                gb_obc_beta = 0.8<br />
                gb_obc_gamma = 4.85<br />
                sa_surface_tension = 2.092</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>tcoupl = berendsen<br />
                tc-grps = System<br />
                tau_t = 0.3<br />
                ref_t = 800<br />
                Pcoupl = no<br />
                Pcoupltype = isotropic<br />
                tau_p = 1<br />
                compressibility = 6.5e-5<br />
                ref_p = 5.0<br />
                refcoord_scaling = No<br />
                andersen_seed = 815131</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>QMMM = no<br />
                QMMM-grps = <br />
                QMmethod = <br />
                QMMMscheme = normal<br />
                QMbasis = <br />
                QMcharge = <br />
                QMmult = <br />
                SH = <br />
                CASorbitals =<br />
                CASelectrons =<br />
                SAon =<br />
                SAoff =<br />
                SAsteps =<br />
                MMChargeScaleFactor = 1<br />
                bOPT =<br />
                bTS =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>annealing =<br />
                annealing_npoints =<br />
                annealing_time =<br />
                annealing_temp =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>gen_vel = yes<br />
                gen_temp = 313<br />
                gen-seed = 173529</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>constraints = none<br />
                constraint_algorithm = Lincs<br />
                continuation = 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</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>energygrp_excl =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>nwall = 0<br />
                wall_type = 9-3<br />
                wall_r_linpot = -1<br />
                wall_atomtype =<br />
                wall_density =<br />
                wall_ewald_zfac = 3</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>pull = no</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>disre = No<br />
                disre-weighting = Conservative<br />
                disre-mixed = no<br />
                disre-fc = 1000<br />
                disre-tau = 0<br />
                nstdisreout = 100<br />
                orire = no<br />
                orire-fc = 0<br />
                orire-tau = 0<br />
                orire-fitgrp =<br />
                nstorireout = 100<br />
                dihre = no<br />
                dihre-fc = 1000</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>free-energy = no<br />
                init-lambda = 0<br />
                delta-lambda = 0<br />
                sc-alpha = 0<br />
                sc-power = 0<br />
                sc-sigma = 0.3<br />
                couple-moltype =<br />
                couple-lambda0 = vdw-q<br />
                couple-lambda1 = vdw-q<br />
                couple-intramol = no</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>acc-grps =<br />
                accelerate =<br />
                freezegrps =<br />
                freezedim =<br />
                cos-acceleration = 0<br />
                deform =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>E-x =<br />
                E-xt =<br />
                E-y =<br />
                E-yt =<br />
                E-z =<br />
                E-zt =</strong> </em></span></p>
        <p>
                <span style="font-size: 14px"><em><strong>user1-grps =<br />
                user2-grps =<br />
                userint1 = 0<br />
                userint2 = 0<br />
                userint3 = 0<br />
                userint4 = 0<br />
                userreal1 = 0<br />
                userreal2 = 0<br />
                userreal3 = 0<br />
                userreal4 = 0<br />
                <span style="display: none"> </span></strong></em></span></p>
        <p>
                Could you tell me which part of the parameter should be changed for Shell MD?<br />
                 <br />
                Your prompt attention to this letter would be highly appreciated.</p>
        <p>
                 Thanks a lot.</p>
        <p>
                 </p>
        <p>
                 Liyan<br />
                <span style="display: none"> </span> <span style="display: none"> </span></p>
        <br />
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