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    On 23/03/2011 3:39 PM, Elisabeth wrote:

    <blockquote

      cite="mid:AANLkTiksd3bUtCr8V6WYRxGWpyZkNAmx+2ouBcXCiQaT@mail.gmail.com"

      type="cite">Thanks Mark for the hints. I am using a pre

      equilibrated box for both runs. Can you again explain how Can I

      interpret this from fluctuations from two runs? Below is the

      resutls from two versions: Thanks!<br>

    </blockquote>

    <br>

    IIRC the contents of the .edr file didn't change across these

    versions, but the reporting of computed quantities did, so I'd make

    my life simpler and use only the 4.5.3 g_energy.<br>

    <br>

    Both simulations have a much higher value for the root-mean-squared

    deviation from the average (i.e. standard deviation) than for the

    average. So that means your data set looks something like "10000 20

    6543 200 23444 23434 15 500 3444". Look at the .xvg file that is

    produced. You need a heck of a lot of such data to have confidence

    that your sample average reflects the true average. If you haven't

    got that pile of data, then you haven't observed the average with

    any confidence. This is normal for quantities computed from

    fluctuations in atomic positions. They're macroscopic quantities,

    and have to be observed over a lot of microscopic configurations.<br>

    <br>

    Be sure to check visually that your system is doing what you hope it

    is doing.<br>

    <br>

    Mark<br>

    <br>

    <blockquote

      cite="mid:AANLkTiksd3bUtCr8V6WYRxGWpyZkNAmx+2ouBcXCiQaT@mail.gmail.com"

      type="cite"><br>

      4.0.7<br>

      <br>

      Statistics over 733801 steps [ 0.0000 thru 1467.6001 ps ], 1 data

      sets<br>

      All averages are exact over 733801 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>

      #Surf*SurfTen&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 203.778&nbsp;&nbsp;&nbsp; 3623.99&nbsp;&nbsp;&nbsp; 3623.98

      -0.00203751&nbsp;&nbsp; -2.99026<br>

      <br>

      <br>

      Statistics over 483401 steps [ 500.0000 thru 1466.8000 ps ], 1

      data sets<br>

      All averages are exact over 483401 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>

      #Surf*SurfTen&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 203.129&nbsp;&nbsp;&nbsp; 3612.58&nbsp;&nbsp;&nbsp; 3612.28&nbsp;&nbsp;

      0.168686&nbsp;&nbsp;&nbsp; 163.086<br>

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

      4.5.3<br>

      <br>

      <br>

      <br>

      Statistics over 732501 steps [ 1.0000 through 1466.0000 ps ], 1

      data sets<br>

      All statistics are over 73251 points<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>

      #Surf*SurfTen&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2374.49&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 570&nbsp;&nbsp;&nbsp; 21081.3&nbsp;&nbsp;

      -3251.38&nbsp; (bar nm)<br>

      <br>

      Statistics over 384501 steps [ 1000.0000 through 1769.0000 ps ], 1

      data sets<br>

      All statistics are over 38451 points<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>

      #Surf*SurfTen&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2610.25&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1000&nbsp;&nbsp;&nbsp; 21109.9&nbsp;&nbsp;&nbsp;

      4638.38&nbsp; (bar nm)<br>

      <br>

      Statistics over 483001 steps [ 500.0000 through 1466.0000 ps ], 1

      data sets<br>

      All statistics are over 48301 points<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>

      #Surf*SurfTen&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1645.07&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 390&nbsp;&nbsp;&nbsp; 20288.3&nbsp;&nbsp;

      -174.289&nbsp; (bar nm)<br>

      <br>

      <br>

      <br>

      <br>

      <br>

      <div class="gmail_quote">On 22 March 2011 23:56, 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 class="im"><br>

            <br>

            <span>On 23/03/11, <b>Elisabeth </b> &lt;<a

                moz-do-not-send="true"

                href="mailto:katesedate@gmail.com" target="_blank">katesedate@gmail.com</a>&gt;

              wrote:</span>

            <blockquote style="border-left: 1px solid rgb(0, 0, 255);

              padding-left: 13px; margin-left: 0pt;" type="cite">

              <div><br>

                <br>

                <div class="gmail_quote">On 22 March 2011 22:46, Justin

                  A. Lemkul <span dir="ltr">&lt;<a

                      moz-do-not-send="true"

                      href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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;">

                    <br>

                    <br>

                    Elisabeth wrote:

                    <div><br>

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

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

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

                        <br>

                        <br>

                        On 22 March 2011 22:31, Justin A. Lemkul &lt;<a

                          moz-do-not-send="true"

                          href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>

                        &lt;mailto:<a moz-do-not-send="true"

                          href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;

                        wrote:<br>

                        <br>

                        <br>

                        <br>

                        &nbsp; &nbsp;Elisabeth wrote:<br>

                        <br>

                        &nbsp; &nbsp; &nbsp; &nbsp;Hello,<br>

                        &nbsp; &nbsp; &nbsp; &nbsp; I did two simulations on the same system

                        using versions 4.0.7<br>

                        &nbsp; &nbsp; &nbsp; &nbsp;and 4.5.3. It seems like the unit of

                        surface tension is not the<br>

                        &nbsp; &nbsp; &nbsp; &nbsp;same in these versions because I am

                        getting ~250 KJ/mol an in<br>

                        &nbsp; &nbsp; &nbsp; &nbsp;4.0.7 and ~ 5000bar nm in 4.5.3?! How

                        KJ/mol can be converted<br>

                        &nbsp; &nbsp; &nbsp; &nbsp;into bar nm? Can anyone help please.<br>

                        <br>

                        <br>

                        &nbsp; &nbsp;Is this from g_energy output? &nbsp;In past

                        versions, everything was<br>

                        &nbsp; &nbsp;printed as "kJ/mol," even quantities that

                        obviously weren't, like<br>

                        &nbsp; &nbsp;temperature, pressure, etc.<br>

                        <br>

                        <br>

                        Yes, so why are the results so different. I am

                        using exactly the same mdp file.! <br>

                        <br>

                      </blockquote>

                      <br>

                    </div>

                    Any pressure-related quantity is going to be subject

                    to enormous fluctuations. This has been discussed

                    within the last few days. &nbsp;Without seeing the .mdp

                    file and a description of the system, it's hard for

                    anyone to comment on what the results might mean.<br>

                  </blockquote>

                  <div><br>

                    Thanks. I am working on a pure alkane system, in a

                    box of 3X3X3 which is extended in Z to create

                    liq/air interface. That is 3X3X6 . What could be

                    reason for such a big difference in results from two

                    version? Thanks alot! &nbsp;&nbsp;</div>

                </div>

              </div>

            </blockquote>

            <br>

          </div>

          Look at the size of the fluctuations printed by g_energy. If

          they're comparable or larger than your differences, then you

          are not observing a statistically significant difference. Over

          just 2ns of a small system, that's likely to be the case.

          Damping such fluctuations requires large simulations or long

          times or both.<br>

          <br>

          You are also generating velocities at the start of this run,

          so probably you are including spurious measurements on

          non-equilibrated configurations in your statistics. If you'd

          thought to tell us your command lines, I wouldn't be guessing

          :-) You can fix this with g_energy -b, but really you should

          separate your equilibration from your production run, even if

          you don't really need to, so that all your workflows have

          similar properties. Then when you come back to repeat some

          analysis in a month's time, you don't have to remember to

          ignore the first 1ns of this simulation...<br>

          <font color="#888888"><br>

            Mark</font>

          <div>

            <div class="h5"><br>

              <br>

              <blockquote style="border-left: 1px solid rgb(0, 0, 255);

                padding-left: 13px; margin-left: 0pt;" type="cite">

                <div>

                  <div class="gmail_quote">

                    <div>

                      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 <br>

                      &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>

                      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>

                      coulombtype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; PME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <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 &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; 1.1 &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; 1.1&nbsp;&nbsp;&nbsp; &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>

                      fourierspacing&nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; 0.12&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;<br>

                      fourier_nx&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; 0<br>

                      fourier_ny&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; 0<br>

                      fourier_nz&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; 0<br>

                      pme_order&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; 4&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>

                      ewald_rtol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 1e-5<br>

                      ;optimize_fft&nbsp;&nbsp;&nbsp; &nbsp; =&nbsp; yes<br>

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

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

                      &nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; <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;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <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<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;"><font

                        color="#888888">

                        <br>

                        -Justin</font>

                      <div>

                        <div><br>

                        </div>

                        <div><br>

                          <br>

                          -- <br>

                          ========================================<br>

                          <br>

                          Justin A. Lemkul<br>

                          Ph.D. Candidate<br>

                          ICTAS Doctoral Scholar<br>

                          MILES-IGERT Trainee<br>

                          Department of Biochemistry<br>

                          Virginia Tech<br>

                          Blacksburg, VA<br>

                          jalemkul[at]<a moz-do-not-send="true"

                            href="http://vt.edu" target="_blank">vt.edu</a>

                          | (540) 231-9080<br>

                          <a moz-do-not-send="true"

                            href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"

                            target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>

                          <br>

                          ========================================<br>

                          -- <br>

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                      </div>

                    </blockquote>

                  </div>

                  <br>

                </div>

              </blockquote>

            </div>

          </div>

          <br>

          --<br>

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