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    On 12/10/2011 3:59 PM, liaoxyi wrote:
    <blockquote
      cite="mid:35cb7096.14ec2.132f67fde2c.Coremail.liaoxyi@163.com"
      type="cite">
      <div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
        14px; font-family: arial;">
        <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
          1.7; font-family: arial;">
          <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
            1.7; font-family: arial;">
            <div>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                TEXT-ALIGN: left; mso-layout-grid-align: none"
                align="left"><span style="mso-bidi-font-size: 10.5pt;
                  mso-font-kerning: 0pt; mso-ansi-language: ZH-CN"><font
                    face="Times New Roman">Hi, dear all,<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                TEXT-ALIGN: left; mso-layout-grid-align: none"
                align="left"><span style="mso-bidi-font-size: 10.5pt;
                  mso-font-kerning: 0pt; mso-ansi-language: ZH-CN"><font
                    face="Times New Roman">I&#8217;m doing the simulation
                    involved in protein and some surface.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                TEXT-ALIGN: left; mso-layout-grid-align: none"
                align="left"><font face="Times New Roman"><span
                    style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                    0pt; mso-ansi-language: ZH-CN">I encounter this
                    problem when trying to use implicit solvent</span><span
                    style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                    0pt" lang="EN-US"> model with GMX<st1:chsdate
                      isrocdate="False" islunardate="False" day="30"
                      month="12" year="1899" w:st="on">4.5.3</st1:chsdate>.<o:p></o:p></span></font></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                TEXT-ALIGN: left; mso-layout-grid-align: none"
                align="left"><span style="mso-bidi-font-size: 10.5pt;
                  mso-font-kerning: 0pt" lang="EN-US"><o:p><font
                      face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                TEXT-ALIGN: left; mso-layout-grid-align: none"
                align="left"><span style="mso-bidi-font-size: 10.5pt;
                  mso-font-kerning: 0pt" lang="EN-US"><font face="Times
                    New Roman">First, minimize. When doing this I got
                    the result as below:<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>0, Dmax=
                    1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>1, Dmax=
                    1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>2, Dmax=
                    1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>4, Dmax=
                    7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>6, Dmax=
                    4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>8, Dmax=
                    2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>10, Dmax=
                    1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>13, Dmax=
                    4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>17, Dmax=
                    7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>19, Dmax=
                    4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>22, Dmax=
                    1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>23, Dmax=
                    1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>27, Dmax=
                    2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Step=<span
                      style="mso-spacerun: yes">&nbsp;&nbsp; </span>29, Dmax=
                    1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04,
                    atom= 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Stepsize too small, or no
                    change in energy.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Converged to machine
                    precision,<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span style="COLOR:
                  #993300; mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">but not to the requested
                    precision Fmax &lt; 1000</font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span style="COLOR:
                  #993300; mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman"><o:p></o:p></font></span>&nbsp;</p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Double precision normally
                    gives you higher accuracy.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">writing lowest energy
                    coordinates.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><o:p><font
                      face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Steepest Descents converged
                    to machine precision in 30 steps,<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">but did not reach the
                    requested Fmax &lt; 1000.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Potential Energy<span
                      style="mso-spacerun: yes">&nbsp; </span>=
                    -2.1852700e+06<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Maximum force<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>=<span
                      style="mso-spacerun: yes">&nbsp; </span>2.6025840e+04
                    on atom 2073<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">Norm of force<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>=<span
                      style="mso-spacerun: yes">&nbsp; </span>2.2667976e+03<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">---------------------------------------</font></span></p>
              <p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span
                  style="" lang="EN-US"><font face="Times New Roman">From
                    above, the force is extremely large. And I don&#8217;t
                    know why.</font></span></p>
            </div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    Nobody can until you have a look at the structure before, during
    (after using nstxout=1) and after the EM, and apply your chemical
    knowledge.<br>
    <br>
    <blockquote
      cite="mid:35cb7096.14ec2.132f67fde2c.Coremail.liaoxyi@163.com"
      type="cite">
      <div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
        14px; font-family: arial;">
        <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
          1.7; font-family: arial;">
          <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
            1.7; font-family: arial;">
            <div>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman"><o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><o:p><font
                      face="Times New Roman">&nbsp;</font></o:p></span><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><o:p><font
                      face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman">the
                    minim.mdp is as below:<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">; minim.mdp - used as input
                    into grompp to generate em.tpr<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">; Parameters describing what
                    to do, when to stop and what to save<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">integrator<span
                      style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= steep<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Algorithm (steep = steepest descent minimization)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">emtol<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    1000.0<span style="mso-spacerun: yes">&nbsp; </span><span
                      style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp; </span>; Stop
                    minimization when the maximum force &lt; 1000.0
                    kJ/mol/nm<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">emstep<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= 0.01<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Energy step size<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">nsteps<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    50000<span style="mso-tab-count: 1">&nbsp; </span><span
                      style="mso-spacerun: yes">&nbsp; </span><span
                      style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp; </span>; Maximum
                    number of (minimization) steps to perform<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><o:p><font
                      face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">; Parameters describing how
                    to find the neighbors of each atom and how to
                    calculate the interactions<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">nstlist<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= 1<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Frequency to update the neighbor list and long range
                    forces<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">ns_type<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= grid<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Method to determine neighbor list (simple, grid)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">rlist<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= 1.0<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Cut-off for making neighbor list (short range
                    forces)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">coulombtype<span
                      style="mso-tab-count: 1">&nbsp;&nbsp; </span>= Cut-off<span
                      style="mso-tab-count: 1"> </span>; for Implicit
                    solvent long-range electrostatics<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">rcoulomb<span
                      style="mso-tab-count: 1"> </span>= 1.0<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Short-range electrostatic cut-off<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">rvdw<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    1.0<span style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Short-range Van der Waals cut-off<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">pbc<span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= xyz <span
                      style="mso-tab-count: 2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>;
                    Periodic Boundary Conditions (yes/no)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">; implicit_solvent<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">implicit_solvent<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= GBSA<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_algorithm<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= OBC<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">nstgbradii<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    1<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">rgbradii<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    1.0<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_epsilon_solvent<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= 78.3<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_obc_alpha<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>= 1<span
                      style="mso-spacerun: yes">&nbsp; </span>; OBC(II)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_obc_beta<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;</span>= 0.8 ;
                    OBC(II)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_obc_gamma<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>=
                    4.85 ; OBC(II)<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt" lang="EN-US"><font
                    face="Times New Roman">gb_dielectric_offset<span
                      style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>= 0.09<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman">-----------------<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span
                  style="" lang="EN-US"><font face="Times New Roman">Is
                    there any item that&#8217;s not proper or needed to add?</font></span></p>
            </div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    Seems fine.<br>
    <br>
    <blockquote
      cite="mid:35cb7096.14ec2.132f67fde2c.Coremail.liaoxyi@163.com"
      type="cite">
      <div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
        14px; font-family: arial;">
        <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
          1.7; font-family: arial;">
          <div style="font-size: 14px; color: rgb(0, 0, 0); line-height:
            1.7; font-family: arial;">
            <div>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman"><o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><o:p><font face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman">Is the
                    minimization necessary for implicit solvent? </font></span></p>
            </div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    Always wise.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:35cb7096.14ec2.132f67fde2c.Coremail.liaoxyi@163.com"
      type="cite">
      <div
        style="line-height:1.7;color:#000000;font-size:14px;font-family:arial">
        <div style="FONT-SIZE: 14px; COLOR: #000000; LINE-HEIGHT: 1.7;
          FONT-FAMILY: arial">
          <div style="FONT-SIZE: 14px; COLOR: #000000; LINE-HEIGHT: 1.7;
            FONT-FAMILY: arial">
            <div>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman">Thank
                    you again for your reading.<o:p></o:p></font></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><o:p><font face="Times New Roman">&nbsp;</font></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><o:p></o:p></span></p>
              <p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt;
                mso-layout-grid-align: none"><span
                  style="mso-bidi-font-size: 10.5pt; mso-font-kerning:
                  0pt" lang="EN-US"><font face="Times New Roman">Kiara</font></span></p>
            </div>
          </div>
        </div>
        <br>
        <br>
        <span title="neteasefooter"><span id="netease_mail_footer"></span></span></div>
      <br>
      <br>
      <span title="neteasefooter"><span id="netease_mail_footer"></span></span><br>
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      <br>
    </blockquote>
    <br>
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