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    On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
    <blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
      type="cite">
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">Dear Gromacs
          Users,</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">I am
          using gromacs version is 4.5.3.<span
            class="apple-converted-space"> and running
            my jobs </span>on single node with 8 cores.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><span
            class="apple-converted-space">I
            have two different systems which</span> contain about 425000
          atoms (protein +
          Lipid +SOL) one with bound ligand&nbsp;</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">and another
          one unbound protein.<span class="apple-converted-space"> &nbsp;</span>I
          have successfully reached up to
          NPT&nbsp;equilibration run step, <br>
        </span></p>
    </blockquote>
    <br>
    It is a poor idea to do equilibration with Parinello-Rahman, which
    is unstable when the system is not already close to equilibrium. For
    some reason people still do it, despite at least a post per week on
    this list suggesting against it, and a warning in the manual. Use
    Berendsen to fix the density, then equilibrate further with P-R to
    get the right ensemble.<br>
    <br>
    <blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
      type="cite">
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">now I want to
          continue the same for production
          run. Without ligand I am able to run successfully But the same
          system with
          ligand is crashing with following error-</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">D D cell
          &nbsp;1 0 0 could only obtain 1520 of the 1521 atoms that are</span>&nbsp;</p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">are&nbsp;</span><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:115%">&nbsp;</span><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:115%">connected via
          constraints from the
          neighbouring cells</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:115%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">This probably
          means your
          constraint length are too long</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">compared
          to</span>&nbsp;<span style="color:rgb(34,34,34);font-family:'Times
          New Roman',serif;font-size:14pt;line-height:115%">the domain
          decomposition
          cell size.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">Decrease
          the number of domain decomposition grid cells or lincs_order</span>.
        <br>
      </p>
    </blockquote>
    <br>
    I'd rather expect your system was blowing up because of the above
    issue. Perhaps the suggestion in the error message is not as
    complete as could be desired - you have so many atoms per processor
    that the constraint length would normally be tiny with respect to
    the cell size. So I think the things you have tried below are
    rearranging the deck chairs on the Titanic.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
      type="cite">
      <span style=""></span>
      <p class="MsoNormal" style="line-height:150%"><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:115%">&nbsp;</span><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:150%">Accordingly
          following the suggestions given in the error I tried to solve
          it with</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          class="apple-converted-space"><span
            style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
            New Roman&quot;,&quot;serif&quot;;color:#222222">Following
            log file and changed,</span></span></p>
      <p class="MsoListParagraphCxSpFirst" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">1.<span
            style="font-family:'Times New
            Roman';font-size:7pt;line-height:normal">&nbsp; &nbsp;&nbsp;</span></span>
        <span style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:19px;line-height:28px;text-indent:0px">1.
          -rcon</span>&nbsp;</p>
      <p class="MsoListParagraphCxSpFirst" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp; &nbsp; &nbsp; &nbsp;
          Estimated maximum distance required for p-lincs was 0.877 thus
          I
          increased it to 0.900</span></p>
      <p class="MsoListParagraphCxSpLast" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;&nbsp;then it
          thrown another error.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;&nbsp;The initial
          cell size (0.877)
          is smaller than the cell size limit (0.900)</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><br>
        </span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">2 .Then</span><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:150%">&nbsp;I tried to
          increase the &#8211;dds and &#8211;rdd from original values
          of 1.25 and 0.623 to 1.30 and 0.670 respectively.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:150%">&nbsp; &nbsp;But it does
          not help </span><span
          style="color:rgb(34,34,34);font-family:'Times New
          Roman',serif;font-size:14pt;line-height:150%">and ended with
          run crash.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;<i><b>What I
              did was logical or I did it wrongly?</b></i></span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><i><b>Now can
              anyone please suggest me the appropriate way to deal with
              the problem mentioned
              above? </b></i></span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">As I want
          the continuation of the same run without altering the output
          after change in
          the parameters (As I have to compare the output with unbound
          protein run thus can&#8217;t
          afford change in output with change in parameters) &nbsp;</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">I know
          that I need to change some of the parameters in .mdp file such
          as </span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">fourierspacing
from
          0.16 to 0.12 and on the contrary increase the pme_order from
          say 4 to 6.</span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><i><b>But as
              asked above by doing so the output will not or will be the
              exact continuation run?</b></i></span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><i><b>How to
              increase the ratio of cell size to constrain length per
              error message?</b></i></span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222"><i><b>If any
              better way of doing so without changing the output please
              suggest,</b></i></span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">I am
          suffering from the same problem since long, </span></p>
      <p class="MsoNormal" style="line-height:150%"><span
          style="font-size:14.0pt;line-height:150%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">Please
          help me .Please see the mdp file for the reference.</span></p>
      <p class="MsoNormal"><span class="apple-converted-space"><span
            style="font-size:10.0pt;line-height:115%;font-family:&quot;Times
            New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;</span></span><span
          style="font-size:10.0pt;line-height:115%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">integrator &nbsp;
          &nbsp; &nbsp; &nbsp;= md</span><br style="">
        <br>
        <span style="">nsteps
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = 10000000</span></p>
      <p class="MsoNormal"><span
          style="font-size:10.0pt;line-height:115%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;dt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = 0.002 &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ; 2 fs</span><br style="">
        <span style="">&gt; &gt;</span><br style="">
        <span style="">&nbsp;; Output
          control</span><br style="">
        <span style="">nstxout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 1000 &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;; <br>
          nstvout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;= 1000 &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;; <br>
          nstxtcout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;= 1000 &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;&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;&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;</span></p>
      <p class="MsoNormal"><span style="">nstenergy &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
          1000 &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;&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;&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;&nbsp;&nbsp;</span></p>
      <p class="MsoNormal"><span style="">&nbsp;nstlog &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp;= 1000 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp;; <br>
          ; Bond parameters<br>
          continuation &nbsp; = yes &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ; Restarting after NPT<br>
          constraint_algorithm = lincs ; holonomic
          constraints<br>
          constraints &nbsp; &nbsp; = all-bonds &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ; all bonds (even heavy atom-H bonds)<br>
          lincs_iter &nbsp; &nbsp; &nbsp; &nbsp; = 1 &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; ; accuracy of LINCS<br>
          lincs_order &nbsp; &nbsp; = 4</span></p>
      <p class="MsoNormal"><span
          style="font-size:10.0pt;line-height:115%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">;
          Neighborsearching</span><br style="">
        <span style="">ns_type &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = grid</span><br style="">
        <span style="">nstlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp;= 5</span>&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;&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;&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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>
      <p class="MsoNormal">&nbsp;rlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= 1.2<br style="">
        <span style="">rcoulomb &nbsp; &nbsp; &nbsp; &nbsp;= 1.2</span><br style="">
        <span style="">rvdw &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp;= 1.2</span><br style="">
        <span style="">; Electrostatics</span><br style="">
        <span style="">coulombtype &nbsp;= PME</span><br style="">
        <span style="">pme_order &nbsp; &nbsp; = 4</span><br style="">
        <span style="">fourierspacing &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          = 0.16</span>&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; &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 style="">
        <span style="">tcoupl &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp;= Nose-Hoover</span><br style="">
        <span style="">tc-grps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= Protein &nbsp;P &nbsp;
          &nbsp;SOL_NA_CL ; <br>
          tau_t &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp;= 0.5 &nbsp; 0.5 &nbsp; &nbsp; &nbsp; 0.5<br>
          ref_t &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp;= 323 323 &nbsp; &nbsp; 323&nbsp;
          group, in K</span><br style="">
        <span style="">; Pressure coupling is on</span><br style="">
        <span style="">pcoupl &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
          Parrinello-Rahman &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;&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;&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;</span></p>
      <p class="MsoNormal"><span style="">pcoupltype &nbsp; &nbsp; = semiisotropic
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; <br>
          tau_p &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp;= 2.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ; time<br>
          ref_p &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; = 1.0 &nbsp; 1.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ; reference<br>
          compressibility = 4.5e-5 &nbsp; &nbsp; &nbsp;
          4.5e-5
;&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;&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;&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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></p>
      <p class="MsoNormal"><span style="">&nbsp;;
          Periodic boundary conditions<br>
          pbc &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= xyz &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;; 3-D
PBC&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;&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;</span></p>
      <p class="MsoNormal"><span style="">&nbsp;; Dispersion correction</span><br
          style="">
        <span style="">DispCorr &nbsp; &nbsp; &nbsp; &nbsp;= EnerPres
          &nbsp; &nbsp;; account for cut-off vdW scheme</span>&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;&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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>
      <p class="MsoNormal">; Velocity generation<br style="">
        <span style="">&nbsp; gen_vel
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = no</span></p>
      <p class="MsoNormal"><span
          style="font-size:10.0pt;line-height:115%;font-family:&quot;Times
          New Roman&quot;,&quot;serif&quot;;color:#222222">&nbsp;</span></p>
      <p class="MsoNormal"><span
          style="line-height:115%;font-family:'Times New
          Roman',serif;color:rgb(34,34,34)"><font size="4">&nbsp;</font></span></p>
      <p class="MsoNormal"><span
          style="line-height:115%;font-family:'Times New
          Roman',serif;color:rgb(34,34,34)"><font size="4">Thanking in
            Advance</font></span></p>
      <br>
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      <br>
    </blockquote>
    <br>
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