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><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                      Average       RMSD     Fluct.      Drift  Tot-Drift<br>-------------------------------------------------------------------------------<br>Density (SI)                 979.37    14.3238    14.2431 -0.0525784   -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 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  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&#39;ll have
    to re-equilibrate once you combine the solvent boxes, don&#39;t bother.<br><font color="#888888">
    <br>
    Mark</font><div><div></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 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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
            </div>
            <div>
              <div>
                &lt;mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;&gt;
                wrote:<br>
                <br>
                   On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan
                wrote:<br>
                <br>
                       Hi Gromacians<br>
                <br>
                       I want to do equilibration of water (spc model)
                first in the NVT<br>
                       ensemble and then in the NPT ensemble to maintain
                a temperature<br>
                       of 300K and a pressure of 1 bar respectively. The
                NVT<br>
                       equilibration works fine and the average
                temperature turns out<br>
                       to be 299.229 K.<br>
                <br>
                       Energy                      Average       RMSD  
                     Fluct.<br>
                             Drift            Tot-Drift<br>
                       ------------------------------<br>
                       -------------------------------------------------<br>
                       Temperature                 299.229    10.3092  
                 10.2463<br>
                         0.0393873    3.93877<br>
                       Heat Capacity Cv:       12.494 J/mol K (factor =
                0.00118698)<br>
                <br>
                         when i do NPT equilibration i am not getting
                the desired<br>
                       pressure as 1 bar or atleast close to 1 bar
                (between 1-1.4 bar).<br>
                       In the mdp file i used semiisotropic pressure
                coupling type<br>
                       because i want to fix the length of the box same
                on two axis as<br>
                       that of the original box size and want to change
                it only on one<br>
                       axis. can any one tell me why iam not getting the
                desired<br>
                       pressure of 1 bar?.<br>
                <br>
                <br>
                   This looks normal for a smallish water system over
                100ps. See<br>
                   <a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
                <br>
                   Mark<br>
                <br>
                <br>
                <br>
                       Energy                      Average       RMSD  
                  Fluct.<br>
                         Drift  Tot-Drift<br>
                     
 -------------------------------------------------------------------------------<br>
                       Pressure (bar)               7.4339    574.052  
                 573.574<br>
                       0.812129    81.2138<br>
                <br>
                       Given below is my mdp file (NPT equilibration).
                any help is<br>
                       highly appreciated.<br>
                <br>
                       title           = DCE NVT equilibration<br>
                       cpp           = usr/bin/cpp<br>
                       integrator   = md<br>
                       nsteps       = 100000<br>
                       dt              = 0.001<br>
                       nstxout       = 100<br>
                       nstvout       = 100<br>
                       nstenergy   = 100<br>
                       nstlog        = 100<br>
                       ns_type     = grid<br>
                       nstlist        = 1<br>
                       rlist            = 1.0<br>
                       coulombtype    = PME<br>
                       rcoulomb         = 1.0<br>
                       vdwtype          = Cut-off<br>
                       rvdw               = 1.0<br>
                       pme_order       = 4<br>
                       fourierspacing  = 0.16<br>
                       pbc                 = xyz<br>
                       tcoupl              = V-rescale<br>
                       tc-grps             = system<br>
                       tau_t                = 0.1<br>
                       ref_t                 = 300<br>
                       pcoupl              = berendsen<br>
                       pcoupltype        = semiisotropic<br>
                       tau_p                = 0.5<br>
                       ref_p                 = 1.0 1.0<br>
                       compressibility   = 0.0 4.5e-5<br>
                       DispCorr            = Enerpres<br>
                       gen_vel             = yes<br>
                       gen_temp          = 300<br>
                       gen_seed          = 173529<br>
                <br>
                       Regards<br>
                       Vinoth<br>
                <br>
                <br>
                   --<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:  +46184714205.<br>
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