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    On 15/04/2011 5:55 AM, Moeed wrote:

    <blockquote

      cite="mid:BANLkTimzQb7uitKW7bo=tq2wq65W_jTiDA@mail.gmail.com"

      type="cite"><br>

      <br>

      <div class="gmail_quote">On 14 April 2011 02:11, Mark Abraham <span

          dir="ltr">&lt;<a moz-do-not-send="true"

            href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span>

        wrote:<br>

        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt

          0.8ex; border-left: 1px solid rgb(204, 204, 204);

          padding-left: 1ex;">

          <div text="#000000" bgcolor="#ffffff">

            <div class="im"> On 14/04/2011 3:40 PM, Moeed wrote:

              <blockquote type="cite"><br>

                <br>

                <div class="gmail_quote">On 13 April 2011 18:45, Mark

                  Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"

                      href="mailto:Mark.Abraham@anu.edu.au"

                      target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>

                  wrote:<br>

                  <blockquote class="gmail_quote" style="margin: 0pt 0pt

                    0pt 0.8ex; border-left: 1px solid rgb(204, 204,

                    204); padding-left: 1ex;">

                    <div text="#000000" bgcolor="#ffffff">

                      <div> On 14/04/2011 10:22 AM, Moeed wrote:

                        <blockquote type="cite">Hello,<br>

                          <br>

                          I have run 2 ns simulations on a hydrocarbon

                          system (initial density of ~ 2 SI and box size

                          is 15 nm), one with version 4.0.7 and the

                          other trial using 4.5.3. Both runs are almost

                          equilibrated to 70 bar pressure but one is

                          giving density of above 600SI (4.0.7) and the

                          other density of around 15 SI (4.5.3). With

                          4.5.3 applying 100 bar pressure does not

                          comrades the system either to the desired

                          density. I need to study the system at

                          different pressures from 1 to 70 bar, and I am

                          wondering if the system can not be compressed

                          with these ref_p values how can I keep the

                          pressure fixed at P &lt; 70 bar!? <br>

                          <br>

                          Please help if you have any idea on why these

                          two versions are giving inconsistent results

                          and which one is reliable.&nbsp; <br>

                        </blockquote>

                        <br>

                      </div>

                      Why are your potential energies positive? What

                      does the final configuration look like? Why aren't

                      you doing a "simulated annealing" style of

                      compression with small increments of delta-P?

                      (These, coincidentally are even good data for your

                      study...) Massive leaps in ensemble conditions are

                      often poorly-conditioned for numerical

                      integration. You're generating velocities that are

                      only approximately correct, not giving them any

                      chance to equilibrate, and then smashing the

                      system with massive over-pressure. Small wonder it

                      might sometimes break...<br>

                    </div>

                  </blockquote>

                  <div><br>

                    Hi Mark,<br>

                    <br>

                    You mean I should get negative potential? I am sure

                    topology is generated properly. can you explain why

                    this is concerning?<br>

                  </div>

                </div>

              </blockquote>

              <br>

            </div>

            What does a set of charges with positive potential energy

            want to do?

            <div class="im"><br>

              <br>

              <blockquote type="cite">

                <div class="gmail_quote">

                  <div> Can you please elaborate on compressing using

                    simulated annealing? How can I do this?<br>

                  </div>

                </div>

              </blockquote>

              <br>

            </div>

            That's not what I said - I used quotation marks and the word

            "style" for a reason. I told you not to do massive changes

            of conditions, and to use small increments of delta-P.

            Equilibrate at one P, change it a bit. Repeat. This is like

            simulated annealing, but with P instead of T.<br>

          </div>

        </blockquote>

        <div><br>

          Dear Mark,<br>

          <br>

          I see now what you mean. But actually my problem is not

          equilibrating..</div>

      </div>

    </blockquote>

    <br>

    Your problem *is* equilibrating. Clearly 4.5.3 is not doing it.<br>

    <br>

    <blockquote

      cite="mid:BANLkTimzQb7uitKW7bo=tq2wq65W_jTiDA@mail.gmail.com"

      type="cite">

      <div class="gmail_quote">

        <div>I can follow your advise and equilibrate the system but as

          I said starting from the same structure and settings, both

          runs one with 4.0.7 and the other 4.5.3, show that system is

          pretty close to ref_p = 70 but densities are terrible

          different. </div>

      </div>

    </blockquote>

    <br>

    Sure, so something got broken in at least one of these. I think

    you're being too rough.<br>

    <br>

    <blockquote

      cite="mid:BANLkTimzQb7uitKW7bo=tq2wq65W_jTiDA@mail.gmail.com"

      type="cite">

      <div class="gmail_quote">

        <div>What I dont realize is that how to judge which version is

          giving correct density. and also version 4.5.3 does not

          compress with any pressure below 100 bar. So even when I

          compress using 4.0.7, and try to use output structure from

          4.0.7 as input for 4.5.3 to apply say ref_p of 70, my box

          expands again.<br>

        </div>

      </div>

    </blockquote>

    <br>

    You're trying to draw deductions based on the doubtful premise that

    you can just apply a massive overpressure and the numerical

    integration will cope. Think about it - massive external pressure

    means lots of collisions and large velocities which mean large

    atomic motions over finite time steps. You've just left the

    integration step the same size, so I'm actually a bit surprised

    4.0.7 appears to have coped. A gentler progressive compression will

    leave the system close to equilibrium throughout, and is much more

    likely to achieve a sensible result.<br>

    <br>

    <blockquote

      cite="mid:BANLkTimzQb7uitKW7bo=tq2wq65W_jTiDA@mail.gmail.com"

      type="cite">

      <div class="gmail_quote">

        <div>I am stuck on this and it seems the only option is to just

          stick to version 4.0.7! <br>

        </div>

      </div>

    </blockquote>

    <br>

    I'm going to stop repeating myself soon :-) I think you're being too

    rough, and that 4.5.3 is getting unlucky and breaking and that 4.0.7

    might be getting lucky.<br>

    <br>

    Mark<br>

    <br>

    <blockquote

      cite="mid:BANLkTimzQb7uitKW7bo=tq2wq65W_jTiDA@mail.gmail.com"

      type="cite">

      <div class="gmail_quote">

        <div>:) <br>

        </div>

        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt

          0.8ex; border-left: 1px solid rgb(204, 204, 204);

          padding-left: 1ex;">

          <div text="#000000" bgcolor="#ffffff"><font color="#888888"> <br>

              Mark</font>

            <div>

              <div class="h5"><br>

                <br>

                <blockquote type="cite">

                  <div class="gmail_quote">

                    <div>Thanks, :)<br>

                      <br>

                      &nbsp;</div>

                    <blockquote class="gmail_quote" style="margin: 0pt

                      0pt 0pt 0.8ex; border-left: 1px solid rgb(204,

                      204, 204); padding-left: 1ex;">

                      <div text="#000000" bgcolor="#ffffff"> <br>

                        When reporting output from .log file and

                        g_energy, please either use plain text email, or

                        switch to a non-proportional font like Courier.

                        Those tables make it harder for people to help

                        you than you want it to be.<br>

                        <font color="#888888"> <br>

                          Mark</font>

                        <div>

                          <div><br>

                            <br>

                            <blockquote type="cite"><br>

                              4.0.7 <br>

                              <br>

                              Statistics over 250001 steps [<b>

                                1500.0001 thru 2000.0001 ps ],</b> 14

                              data sets<br>

                              The term 'Cons. rmsd ()' is averaged over

                              2501 frames<br>

                              All other averages are exact over 250001

                              steps<br>

                              <br>

                              Energy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Average&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              RMSD&nbsp;&nbsp;&nbsp;&nbsp; Fluct.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Drift&nbsp; Tot-Drift<br>

-------------------------------------------------------------------------------<br>

                              Angle&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 36.9945&nbsp;&nbsp;

                              0.806738&nbsp;&nbsp; 0.804483&nbsp; 0.0521993&nbsp;&nbsp; 0.208798<br>

                              Ryckaert-Bell.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.04227&nbsp;&nbsp;

                              0.376253&nbsp;&nbsp; 0.371412&nbsp; 0.0521057&nbsp;&nbsp; 0.208424<br>

                              LJ-14&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.23048&nbsp;&nbsp;

                              0.119612&nbsp;&nbsp; 0.119611 0.00033983 0.00135933<br>

                              Coulomb-14&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.66329&nbsp;&nbsp;

                              0.104171&nbsp;&nbsp; 0.102175&nbsp; 0.0175753&nbsp; 0.0703015<br>

                              LJ (SR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              -27.3967&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;

                              0.0421934&nbsp;&nbsp; 0.168774<br>

                              Coulomb (SR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.98711&nbsp;&nbsp;

                              0.163579&nbsp;&nbsp;&nbsp; 0.16062 -0.0268199&nbsp;&nbsp; -0.10728<br>

                              Potential&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              31.1944&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp; 0.137594&nbsp;&nbsp;

                              0.550377<br>

                              Kinetic En.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 51.1009&nbsp;&nbsp;

                              0.987759&nbsp;&nbsp; 0.987724 0.00725949&nbsp; 0.0290381<br>

                              Total Energy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              82.2953&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp; 0.144851&nbsp;&nbsp;

                              0.579408<br>

                              Temperature&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 299.98&nbsp;&nbsp;&nbsp;

                              5.79849&nbsp;&nbsp;&nbsp; 5.79828 0.000340897&nbsp;&nbsp; 0.170449<br>

                              <b>Pressure (bar)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 69.3587&nbsp;&nbsp;&nbsp;

                                414.279&nbsp;&nbsp;&nbsp; 414.256&nbsp; 0.0298385&nbsp;&nbsp;&nbsp; 14.9193</b><br>

                              Cons. rmsd ()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4.01744e-06

                              1.41883e-07 1.41883e-07&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>

                              <b>Box-X&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                                3.04882&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0

                                3.57512e-06 0.00178757<br>

                                Box-Y&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                                3.04882&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 3.57512e-</b><br>

                              <br>

                              <br>

                              -----------------------------<br>

                              4.5.3. <br>

                              <br>

                              [<b> 1500.0001 thru 2000.0001 ps ],</b><br>

                              <br>

                              Energy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Average&nbsp;&nbsp;

                              Err.Est.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RMSD&nbsp; Tot-Drift<br>

-------------------------------------------------------------------------------<br>

                              Angle&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 37.1357&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.071&nbsp;&nbsp; 0.812307&nbsp; -0.099711&nbsp; (kJ/mol)<br>

                              Ryckaert-Bell.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.17677&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.14&nbsp;&nbsp; 0.445934&nbsp; -0.529281&nbsp; (kJ/mol)<br>

                              LJ-14&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.18878&nbsp;&nbsp;&nbsp;&nbsp;

                              0.0087&nbsp;&nbsp; 0.137673&nbsp;&nbsp; -0.03119&nbsp; (kJ/mol)<br>

                              Coulomb-14&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.60372&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.051&nbsp;&nbsp; 0.126405&nbsp; -0.144403&nbsp; (kJ/mol)<br>

                              LJ (SR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -4.24478&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.29&nbsp;&nbsp; 0.742141&nbsp;&nbsp; 0.697187&nbsp; (kJ/mol)<br>

                              Coulomb (SR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.97451&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.082&nbsp;&nbsp; 0.198278&nbsp;&nbsp; 0.232025&nbsp; (kJ/mol)<br>

                              Potential&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 54.6272&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.31&nbsp;&nbsp;&nbsp; 1.20733&nbsp;&nbsp; 0.124627&nbsp; (kJ/mol)<br>

                              Kinetic En.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 51.1047&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.021&nbsp;&nbsp;&nbsp;&nbsp; 0.9945&nbsp; -0.066306&nbsp; (kJ/mol)<br>

                              Total Energy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 105.732&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.31&nbsp;&nbsp;&nbsp; 1.58869&nbsp;&nbsp; 0.058321&nbsp; (kJ/mol)<br>

                              Temperature&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 300.002&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              0.12&nbsp;&nbsp;&nbsp; 5.83806&nbsp; -0.389239&nbsp; (K)<br>

                              <b>Pressure&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                                66.734&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 91.83&nbsp;&nbsp;&nbsp; 11.5294&nbsp;

                                (bar)</b><br>

                              Constr. rmsd&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.2661e-10&nbsp;&nbsp;&nbsp;

                              2.3e-10 3.58302e-08 -1.3595e-09&nbsp; ()<br>

                              <b>Box-X&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                                11.0055&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.082&nbsp;&nbsp; 0.175309&nbsp;

                                -0.496198&nbsp; (nm)<br>

                                Box-Y&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 11.0055&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                                0.082&nbsp;&nbsp; 0.175309&nbsp; -0.496198&nbsp; (nm)</b><br>

                              <br>

                              <br>

                              <br>

                              <br>

                              &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              <br>

                              pbc&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; xyz<br>

                              &nbsp; <br>

                              integrator&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; md&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>

                              dt&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 0.002&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp; &nbsp;<br>

                              nsteps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1000000 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; <br>

                              nstcomm&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 100&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;<br>

                              nstenergy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 100 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;<br>

                              nstxout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 100&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              <br>

                              nstlist&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 10&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              ns_type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; grid&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              <br>

                              coulombtype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; Shift<br>

                              vdw-type&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; Shift&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              rcoulomb-switch&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;<br>

                              rvdw-switch&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 0.9 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              rlist&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1.2&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              rcoulomb&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1.2 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; <br>

                              rvdw&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1.0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              <br>

                              Tcoupl&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; v-rescale&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              tc-grps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; System&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;<br>

                              tau_t&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 0.1&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              ref_t&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 300&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              &nbsp;<br>

                              <br>

                              Pcoupl&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; berendsen<br>

                              Pcoupltype&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp;

                              isotropic&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>

                              tau_p&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp;&nbsp; <br>

                              compressibility&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 4.5e-5 4.5e-5&nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp; <br>

                              ref_p&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 70&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              <br>

                              <br>

                              gen_vel&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; yes&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              <br>

                              gen_temp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 300.0&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp; <br>

                              gen_seed&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 173529&nbsp;&nbsp;&nbsp; &nbsp; <br>

                              <br>

                              <br>

                              constraints&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; = all-bonds&nbsp;&nbsp;&nbsp;

                              &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>

                              constraint-algorithm = lincs&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>

                              <br>

                            </blockquote>

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