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    actually, as far as i know, the -DFLEXIBLE argument has no effect on
    simulations without explicit water ?!<br>
    <br>
    i just copied the "define" line from my explicit simulation systems
    .. so, the only define value, that has a meaning is -DPOSRESHELIX.<br>
    <br>
    i didn't use constraints for the first time in my life since
    implicit solvent simulations incorporate a much smaller number of
    atoms and are therefore not that expensive computationally. i always
    use this setting for my explicit simulations only in order to
    increase the step size to 2fs with a clear conscience ...<br>
    <br>
    best wishes<br>
    vedat<br>
    <br>
    <br>
    Am 28.02.2012 15:18, schrieb Steven Neumann:
    <blockquote
cite="mid:CAKZJqQFJ9B56j398CaezyTJbvPeSJmk79KQ_z+dChx_Q5qoaVA@mail.gmail.com"
      type="cite">
      <div>Thank you all!</div>
      <div>&nbsp;</div>
      <div>How about -DFLEXIBLE in both em and md?</div>
      <div>&nbsp;</div>
      <div>Steven<br>
        <br>
      </div>
      <div class="gmail_quote">On Tue, Feb 28, 2012 at 2:13 PM, Justin
        A. Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span>
        wrote:<br>
        <blockquote style="border-left: 1px solid rgb(204, 204, 204);
          margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
          class="gmail_quote">
          <div class="im"><br>
            <br>
            lina wrote:<br>
            <blockquote style="border-left: 1px solid rgb(204, 204,
              204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
              class="gmail_quote">On Tue, Feb 28, 2012 at 10:07 PM,
              Steven Neumann &lt;<a moz-do-not-send="true"
                href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>&gt;
              wrote:<br>
              <blockquote style="border-left: 1px solid rgb(204, 204,
                204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
                class="gmail_quote">Thank you Vedat!<br>
                <br>
                Why do you use -DFLEXIBLE in md and in em?<br>
                Why dont you use constraint algorithm (LINCS) in your
                simulation?<br>
              </blockquote>
              <br>
              Otherwise, the system is easily explode with lots of LINCS
              warning.<br>
              <br>
            </blockquote>
            <br>
          </div>
          A system that is unstable will cause the LINCS algorithm to
          fail, but turning off constraints does not prevent a system
          from becoming unstable or crashing.<br>
          <br>
          -Justin
          <div>
            <div class="h5"><br>
              <br>
              <blockquote style="border-left: 1px solid rgb(204, 204,
                204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
                class="gmail_quote">Also thanks Vedat for sharing,<br>
                <br>
                Best regards,<br>
                <br>
                <blockquote style="border-left: 1px solid rgb(204, 204,
                  204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
                  class="gmail_quote">Steven<br>
                  <br>
                  On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz &lt;<a
                    moz-do-not-send="true" href="mailto:durmaz@zib.de"
                    target="_blank">durmaz@zib.de</a>&gt; wrote:<br>
                  <blockquote style="border-left: 1px solid rgb(204,
                    204, 204); margin: 0px 0px 0px 0.8ex; padding-left:
                    1ex;" class="gmail_quote"><br>
                    hi steven,<br>
                    <br>
                    i've been simulating a 33 AA peptide for the past
                    two days using implicent<br>
                    solvent in order to achieve a proper folding.<br>
                    <br>
                    i haven't added counterions, however, the systems
                    shows nice results<br>
                    according to what i've expected. the mdrun command
                    (for the extension) for<br>
                    our hardware looks as follows:<br>
                    <br>
                    mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi
                    md.cpt -deffnm md 2&gt;&amp;1<br>
                    <br>
                    and here's the mdp file for the energy minimization:<br>
                    <br>
                    define &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;-DFLEXIBLE<br>
                    constraints &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;none<br>
                    integrator &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;steep<br>
                    dt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0.001 &nbsp; &nbsp;; ps<br>
                    nsteps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;30000<br>
                    vdwtype &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;cut-off<br>
                    coulombtype &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;cut-off<br>
                    pbc &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;no<br>
                    nstlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0<br>
                    ns_type &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;simple<br>
                    rlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; &nbsp; ; this means
                    all-vs-all (no cut-off), which<br>
                    gets expensive for bigger systems<br>
                    rcoulomb &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0<br>
                    rvdw &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0<br>
                    comm-mode &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;angular<br>
                    comm-grps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;Protein<br>
                    optimize_fft &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;yes<br>
                    ;<br>
                    ; &nbsp; &nbsp; &nbsp; Energy minimizing stuff<br>
                    ;<br>
                    emtol &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;5.0<br>
                    emstep &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0.01<br>
                    ;<br>
                    ; Implicit solvent<br>
                    ;<br>
                    implicit_solvent &nbsp; &nbsp;= &nbsp;GBSA<br>
                    gb_algorithm &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;Still ; HCT ; OBC<br>
                    nstgbradii &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1<br>
                    rgbradii &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0 &nbsp; ; [nm] Cut-off for the
                    calculation of the Born<br>
                    radii. Currently must be equal to rlist<br>
                    gb_epsilon_solvent &nbsp;= &nbsp;80 &nbsp; &nbsp;; Dielectric constant
                    for the implicit<br>
                    solvent<br>
                    ; gb_saltconc &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; ; Salt concentration
                    for implicit solvent<br>
                    models, currently not used<br>
                    sa_algorithm &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;Ace-approximation<br>
                    sa_surface_tension &nbsp;= -1<br>
                    <br>
                    <br>
                    and for the md run:<br>
                    <br>
                    define &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;-DPOSRESHELIX ; -DFLEXIBLE
                    -DPOSRES<br>
                    constraints &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;none<br>
                    integrator &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;md<br>
                    dt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0.001 &nbsp; ; ps<br>
                    nsteps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1000000000 ; 100000 ps = 100
                    ns<br>
                    nstcomm &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;10<br>
                    nstcalcenergy &nbsp; &nbsp; &nbsp; = &nbsp;10<br>
                    nstxout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;1000 &nbsp; &nbsp; ; frequency to write
                    coordinates to output<br>
                    trajectory<br>
                    nstvout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; &nbsp; ; frequency to write
                    velocities to output<br>
                    trajectory; the last velocities are always written<br>
                    nstfout &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; &nbsp; ; frequency to write
                    forces to output<br>
                    trajectory<br>
                    nstlog &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1000 &nbsp; &nbsp; &nbsp; &nbsp; ; frequency to
                    write energies to log<br>
                    file<br>
                    nstenergy &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;1000 &nbsp; &nbsp; ; frequency to write
                    energies to edr file<br>
                    <br>
                    vdwtype &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;cut-off<br>
                    coulombtype &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;cut-off<br>
                    <br>
                    pbc &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;no<br>
                    <br>
                    nstlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0<br>
                    ns_type &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;simple<br>
                    rlist &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; &nbsp; ; this means
                    all-vs-all (no cut-off), which<br>
                    gets expensive for bigger systems<br>
                    rcoulomb &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0<br>
                    rvdw &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0<br>
                    <br>
                    comm-mode &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;angular<br>
                    comm-grps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;system<br>
                    <br>
                    optimize_fft &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;yes<br>
                    <br>
                    ; V-rescale temperature coupling is on<br>
                    Tcoupl &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;v-rescale<br>
                    tau_t &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;0.1<br>
                    tc_grps &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;system<br>
                    ref_t &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;300<br>
                    ; Pressure coupling is off<br>
                    Pcoupl &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;no<br>
                    ; Generate velocites is on<br>
                    gen_vel &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;yes<br>
                    gen_temp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;300<br>
                    gen_seed &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;-1<br>
                    <br>
                    ;<br>
                    ; Implicit solvent<br>
                    ;<br>
                    implicit_solvent &nbsp; &nbsp;= &nbsp;GBSA<br>
                    gb_algorithm &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;Still ; HCT ; OBC<br>
                    nstgbradii &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;1<br>
                    rgbradii &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;0 &nbsp; ; [nm] Cut-off for the
                    calculation of the Born<br>
                    radii. Currently must be equal to rlist<br>
                    gb_epsilon_solvent &nbsp;= &nbsp;80 &nbsp; &nbsp;; Dielectric constant
                    for the implicit<br>
                    solvent<br>
                    ; gb_saltconc &nbsp; &nbsp; &nbsp; = &nbsp;0 &nbsp; &nbsp; ; Salt concentration
                    for implicit solvent<br>
                    models, currently not used<br>
                    sa_algorithm &nbsp; &nbsp; &nbsp; &nbsp;= &nbsp;Ace-approximation<br>
                    sa_surface_tension &nbsp;= -1<br>
                    <br>
                    <br>
                    best regards,<br>
                    vedat<br>
                    <br>
                    <br>
                    Am 28.02.2012 11:59, schrieb Steven Neumann:<br>
                    <br>
                    <blockquote style="border-left: 1px solid rgb(204,
                      204, 204); margin: 0px 0px 0px 0.8ex;
                      padding-left: 1ex;" class="gmail_quote">Dear Gmx
                      Users,<br>
                      I am using Gromacs 4.5.4 and I would like to
                      implement implicit solvent<br>
                      for folding of my protein. I read mailing list and
                      it is still confusing for<br>
                      me.<br>
                      Is it proper to use counterions within the system?
                      If not, how can I<br>
                      obtain netral system?<br>
                      Do we use cut off for vdw and coulombic
                      interactions?<br>
                      What kind of integrator should be used with a
                      timestep?<br>
                      I will appreciate an mdp file for protein folding!
                      Thank you<br>
                      Steven<br>
                    </blockquote>
                    --<br>
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              -- <br>
            </div>
          </div>
          ========================================<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> | <a moz-do-not-send="true"
            href="tel:%28540%29%20231-9080" target="_blank"
            value="+15402319080">(540) 231-9080</a><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>
          ========================================
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