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    On 29/10/2010 7:50 PM, vinothkumar mohanakrishnan wrote:

    <blockquote

      cite="mid:AANLkTimn0aVxOyH=sscZds8fCOTcXhWp1pLkdrCKsKhP@mail.gmail.com"

      type="cite">Hi Mark<br>

      <br>

      How come 7 +/- 500 bar is approximately 1 bar. Can you explain it

      more clearly? It will be of more useful to me to understand the

      concept.<br>

    </blockquote>

    <br>

    It's a pretty basic one in scientific measurement. See

    <a class="moz-txt-link-freetext" href="http://en.wikipedia.org/wiki/Error_bar">http://en.wikipedia.org/wiki/Error_bar</a> and links thereon, or an

    introductory physics text.<br>

    <br>

    When we make a measurement, that's only an estimate of the true

    value. When someone cites a range of uncertainty, they are

    acknowledging that there is an appreciable chance that the true

    value, of which they have taken an error-prone measurement, lies

    somewhere in a given range. So if 7 +/-500 acknowledges that the

    true value could lie anywhere from about -493 to 507, then that's

    not much less useful than an observation of 1 +/- 500, which

    acknowledges that the true value could lie anywhere from about -499

    to 501. The details of that chance will vary with exactly what

    variation quantity is being reported (standard deviation, standard

    error, maximum deviation, quartile, etc.).<br>

    <br>

    Here, g_energy is effectively reporting that the instantaneous

    pressure values varied over a range of many hundreds of bar, and

    that you haven't made enough observations to report a reliable

    average.<br>

    <br>

    Mark<br>

    <br>

    <blockquote

      cite="mid:AANLkTimn0aVxOyH=sscZds8fCOTcXhWp1pLkdrCKsKhP@mail.gmail.com"

      type="cite"><br>

      One more thing, density (from g_energy command) of water is found

      to low (expected 1000) after NPT is equilibration. why? given

      below is my average density value. Can i proceed with this density

      value?<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>

      Density (SI)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 979.37&nbsp;&nbsp;&nbsp; 14.3238&nbsp;&nbsp;&nbsp; 14.2431

      -0.0525784&nbsp;&nbsp; -5.25789<br>

      <br>

      Regards<br>

      Vinoth<br>

      <br>

      <div class="gmail_quote">On Fri, Oct 29, 2010 at 2:06 PM, 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 29/10/2010 6:39 PM, vinothkumar

              mohanakrishnan wrote:

              <blockquote type="cite">I am using the semiisotropic

                pressure scaling because i want the box size to remain

                the same as that of the original box size in X and Y

                axis and want to change it only on the Z axis. I am

                doing this because at a latter stage i want to create an

                interface with organic solvent where i need the cross

                sections (X and Y axis length) of both the box should be

                the same.<br>

                <br>

                what i should do now&nbsp; get the pressure of 1 bar?<br>

              </blockquote>

              <br>

            </div>

            7 +/- 500 *is* approximately 1 bar, and hardly any better an

            approximation than 1 +/- 500. If you want lower

            fluctuations, use a larger system and run for a much longer

            time. Or, since you'll have to re-equilibrate once you

            combine the solvent boxes, don't bother.<br>

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

              Mark</font>

            <div>

              <div class="h5"><br>

                <blockquote type="cite"><br>

                  Has no one has got the pressure of water to be close

                  to 1 bar in GROMACS till now?<br>

                  <br>

                  Regards<br>

                  Vinoth<br>

                  <br>

                  <div class="gmail_quote">On Fri, Oct 29, 2010 at 12:54

                    PM, David van der Spoel <span dir="ltr">&lt;<a

                        moz-do-not-send="true"

                        href="mailto:spoel@xray.bmc.uu.se"

                        target="_blank">spoel@xray.bmc.uu.se</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>On 2010-10-29 09.08, vinothkumar

                        mohanakrishnan 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>

                          Hi Mark<br>

                          <br>

                          I read the link before posting the question.

                          even though the fluctation<br>

                          is between 500-600 (as said in the link) bar

                          the average pressure is<br>

                          around 7.4 bar. my concern is the average

                          pressure?. Because at a latter<br>

                          stage i am going to combine this water box

                          with another organic solvent<br>

                          and i want to avoid any complications there.<br>

                        </blockquote>

                        <br>

                      </div>

                      Think again of what you just wrote. Your value is

                      7 +/- 500. In fact according to normal statistical

                      rules you should round the value of 7 to 0. If you

                      want more accurate number you could increase the

                      box size by a factor of 100.<br>

                      <br>

                      By the way, why are you using semiisotropic

                      pressure scaling in a water box?<br>

                      <br>

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

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

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

                        <div> <br>

                          Regards<br>

                          Vinoth<br>

                          <br>

                          On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham

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

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

                            target="_blank">Mark.Abraham@anu.edu.au</a><br>

                        </div>

                        <div>

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

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

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

                            wrote:<br>

                            <br>

                            &nbsp; &nbsp;On 29/10/2010 5:48 PM, vinothkumar

                            mohanakrishnan wrote:<br>

                            <br>

                            &nbsp; &nbsp; &nbsp; &nbsp;Hi Gromacians<br>

                            <br>

                            &nbsp; &nbsp; &nbsp; &nbsp;I want to do equilibration of water

                            (spc model) first in the NVT<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;ensemble and then in the NPT ensemble

                            to maintain a temperature<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;of 300K and a pressure of 1 bar

                            respectively. The NVT<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;equilibration works fine and the

                            average temperature turns out<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;to be 299.229 K.<br>

                            <br>

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

                            &nbsp; &nbsp; RMSD &nbsp; &nbsp; &nbsp; &nbsp;Fluct.<br>

                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Drift &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Tot-Drift<br>

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

                            &nbsp; &nbsp; &nbsp;

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

                            &nbsp; &nbsp; &nbsp; &nbsp;Temperature &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 299.229 &nbsp;

                            &nbsp;10.3092 &nbsp; &nbsp;10.2463<br>

                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.0393873 &nbsp; &nbsp;3.93877<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;Heat Capacity Cv: &nbsp; &nbsp; &nbsp; 12.494 J/mol

                            K (factor = 0.00118698)<br>

                            <br>

                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;when i do NPT equilibration i am

                            not getting the desired<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;pressure as 1 bar or atleast close to

                            1 bar (between 1-1.4 bar).<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;In the mdp file i used semiisotropic

                            pressure coupling type<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;because i want to fix the length of

                            the box same on two axis as<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;that of the original box size and

                            want to change it only on one<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;axis. can any one tell me why iam not

                            getting the desired<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;pressure of 1 bar?.<br>

                            <br>

                            <br>

                            &nbsp; &nbsp;This looks normal for a smallish water

                            system over 100ps. See<br>

                            &nbsp; &nbsp;<a moz-do-not-send="true"

                              href="http://www.gromacs.org/Documentation/Terminology/Pressure"

                              target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>

                            <br>

                            &nbsp; &nbsp;Mark<br>

                            <br>

                            <br>

                            <br>

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

                            &nbsp; &nbsp; RMSD &nbsp; &nbsp; Fluct.<br>

                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Drift &nbsp;Tot-Drift<br>

                            &nbsp; &nbsp; &nbsp;

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

                            &nbsp; &nbsp; &nbsp; &nbsp;Pressure (bar) &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 7.4339 &nbsp;

                            &nbsp;574.052 &nbsp; &nbsp;573.574<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;0.812129 &nbsp; &nbsp;81.2138<br>

                            <br>

                            &nbsp; &nbsp; &nbsp; &nbsp;Given below is my mdp file (NPT

                            equilibration). any help is<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;highly appreciated.<br>

                            <br>

                            &nbsp; &nbsp; &nbsp; &nbsp;title &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = DCE NVT

                            equilibration<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;cpp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = usr/bin/cpp<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;integrator &nbsp; = md<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nsteps &nbsp; &nbsp; &nbsp; = 100000<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;dt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 0.001<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nstxout &nbsp; &nbsp; &nbsp; = 100<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nstvout &nbsp; &nbsp; &nbsp; = 100<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nstenergy &nbsp; = 100<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nstlog &nbsp; &nbsp; &nbsp; &nbsp;= 100<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;ns_type &nbsp; &nbsp; = grid<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;nstlist &nbsp; &nbsp; &nbsp; &nbsp;= 1<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;rlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 1.0<br>

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

                            &nbsp; &nbsp; &nbsp; &nbsp;rcoulomb &nbsp; &nbsp; &nbsp; &nbsp; = 1.0<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;vdwtype &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= Cut-off<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;rvdw &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = 1.0<br>

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

                            &nbsp; &nbsp; &nbsp; &nbsp;fourierspacing &nbsp;= 0.16<br>

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

                            &nbsp; &nbsp; &nbsp; &nbsp;tcoupl &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= V-rescale<br>

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

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

                            &nbsp; &nbsp; &nbsp; &nbsp;ref_t &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = 300<br>

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

                            &nbsp; &nbsp; &nbsp; &nbsp;pcoupltype &nbsp; &nbsp; &nbsp; &nbsp;= semiisotropic<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;tau_p &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 0.5<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;ref_p &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = 1.0 1.0<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;compressibility &nbsp; = 0.0 4.5e-5<br>

                            &nbsp; &nbsp; &nbsp; &nbsp;DispCorr &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= Enerpres<br>

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

                            &nbsp; &nbsp; &nbsp; &nbsp;gen_temp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 300<br>

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

                            <br>

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

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

                            <br>

                            <br>

                            &nbsp; &nbsp;--<br>

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                      </blockquote>

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

                        <br>

                        -- <br>

                        David van der Spoel, Ph.D., Professor of Biology<br>

                        Dept. of Cell &amp; Molec. Biol., Uppsala

                        University.<br>

                        Box 596, 75124 Uppsala, Sweden. Phone:

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                            href="mailto:gmx-users-request@gromacs.org"

                            target="_blank">gmx-users-request@gromacs.org</a>.<br>

                          Can't post? Read <a moz-do-not-send="true"

                            href="http://www.gromacs.org/Support/Mailing_Lists"

                            target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>

                        </div>

                      </div>

                    </blockquote>

                  </div>

                  <br>

                </blockquote>

                <br>

              </div>

            </div>

          </div>

          <br>

          --<br>

          gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"

            href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>

          <a moz-do-not-send="true"

            href="http://lists.gromacs.org/mailman/listinfo/gmx-users"

            target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>

          Please search the archive at <a moz-do-not-send="true"

            href="http://www.gromacs.org/Support/Mailing_Lists/Search"

            target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>

          before posting!<br>

          Please don't post (un)subscribe requests to the list. Use the<br>

          www interface or send it to <a moz-do-not-send="true"

            href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>

          Can't post? Read <a moz-do-not-send="true"

            href="http://www.gromacs.org/Support/Mailing_Lists"

            target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>

        </blockquote>

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