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    On 28/10/2010 3:03 AM, Sai Pooja wrote:
    <blockquote
      cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
      type="cite">
      <div>Hi Mark,</div>
      <div>&nbsp;</div>
      <div>I am familiar with the section, however, I have a few doubts.</div>
      <div>&nbsp;</div>
      <div>When you say ...</div>
      <div>So modified protein-water VDW interactions can be introduced
        by defining all relevant "protein atom"-"TIP3P oxygen"
        [nonbond_params] terms.</div>
      <div>Do you mean that I can introduce [pairtypes] specifying
        interactions of all "relevant protein atoms" with "tip3p atoms"?</div>
    </blockquote>
    No, [pairtypes] are not relevant.<br>
    <blockquote
      cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
      type="cite">
      <div>&nbsp;</div>
      <div>&nbsp;</div>
      <div>and I do not understand - It may be simpler to modify the
        [atomtypes] to generate the "modified" VDW from the combination
        rule</div>
      <div>Would this not alter all non-bonded interactions for the
        atomtypes defined? I think I haven't understood thsi properly...</div>
    </blockquote>
    <br>
    I was thinking of a flawed procedure. Ignore this part.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
      type="cite">
      <div>&nbsp;</div>
      <div>&nbsp;</div>
      <div>Pooja</div>
      <div><br>
        &nbsp;</div>
      <div class="gmail_quote">On Tue, Oct 26, 2010 at 8:21 PM, Mark
        Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="padding-left: 1ex;
          margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
          204, 204);">I think manual 5.3.3 covers the relevant points.
          Let me know what is not clear.<br>
          <font color="#888888"><br>
            Mark</font>
          <div><br>
            <br>
            ----- Original Message -----<br>
            From: Sai Pooja &lt;<a moz-do-not-send="true"
              href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>&gt;<br>
          </div>
          <div>
            <div>Date: Wednesday, October 27, 2010 9:41<br>
              Subject: Re: [gmx-users] Forcefield parameters<br>
              To: Discussion list for GROMACS users &lt;<a
                moz-do-not-send="true"
                href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>
              <br>
              <font style="font-weight: normal; font-size: 14px;
                font-style: normal; background-color: rgb(245, 248,
                240);">&gt; </font><br>
              <font style="font-weight: normal; font-size: 14px;
                font-style: normal; background-color: rgb(245, 248,
                240);">&gt; </font><br>
              <div class="gmail_quote"><font style="font-weight: normal;
                  font-size: 14px; font-style: normal; background-color:
                  rgb(245, 248, 240);">&gt; </font>On Tue, Oct 26, 2010
                at 6:04 PM, Mark Abraham <span dir="ltr">&lt;<a
                    moz-do-not-send="true">mark.abraham@anu.edu.au</a>&gt;</span>
                wrote:<br>
                <blockquote class="gmail_quote" style="padding-left:
                  1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid
                  rgb(204, 204, 204);">
                  <div><font style="font-weight: normal; font-size:
                      14px; font-style: normal; background-color:
                      rgb(245, 248, 240);">&gt; </font><br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font><br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font>----- Original Message
                    -----<br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font>From: Sai Pooja &lt;<a
                      moz-do-not-send="true">saipooja@gmail.com</a>&gt;<br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font>Date: Wednesday, October
                    27, 2010 8:52<br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font>Subject: Re: [gmx-users]
                    Forcefield parameters<br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font>To: Discussion list for
                    GROMACS users &lt;<a moz-do-not-send="true">gmx-users@gromacs.org</a>&gt;<br>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font><br>
                    <div class="gmail_quote"><font style="font-weight:
                        normal; font-size: 14px; font-style: normal;
                        background-color: rgb(245, 248, 240);"><font
                          style="font-weight: normal; font-size: 14px;
                          font-style: normal; background-color: rgb(245,
                          248, 240);">&gt; </font>&gt; </font>On Tue,
                      Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <span
                        dir="ltr">&lt;<a moz-do-not-send="true">jalemkul@vt.edu</a>&gt;</span>
                      wrote:<br>
                      <blockquote class="gmail_quote"
                        style="padding-left: 1ex; margin: 0px 0px 0px
                        0.8ex; border-left: 1px solid rgb(204, 204,
                        204);"><font style="font-weight: normal;
                          font-size: 14px; font-style: normal;
                          background-color: rgb(245, 248, 240);"><font
                            style="font-weight: normal; font-size: 14px;
                            font-style: normal; background-color:
                            rgb(245, 248, 240);">&gt; </font>&gt; </font><br>
                        <font style="font-weight: normal; font-size:
                          14px; font-style: normal; background-color:
                          rgb(245, 248, 240);"><font style="font-weight:
                            normal; font-size: 14px; font-style: normal;
                            background-color: rgb(245, 248, 240);">&gt;
                          </font>&gt; </font><br>
                        <font style="font-weight: normal; font-size:
                          14px; font-style: normal; background-color:
                          rgb(245, 248, 240);"><font style="font-weight:
                            normal; font-size: 14px; font-style: normal;
                            background-color: rgb(245, 248, 240);">&gt;
                          </font>&gt; </font>Sai Pooja wrote:
                        <div><br>
                          <blockquote class="gmail_quote"
                            style="padding-left: 1ex; margin: 0px 0px
                            0px 0.8ex; border-left: 1px solid rgb(204,
                            204, 204);"><font style="font-weight:
                              normal; font-size: 14px; font-style:
                              normal; background-color: rgb(245, 248,
                              240);"><font style="font-weight: normal;
                                font-size: 14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>On Tue, Oct 26, 2010
                            at 3:46 PM, Justin A. Lemkul &lt;<a
                              moz-do-not-send="true">jalemkul@vt.edu</a>
                            &lt;mailto:<a moz-do-not-send="true">jalemkul@vt.edu</a>&gt;&gt;
                            wrote:<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp;Sai Pooja wrote:<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;Hi,<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp; I want to
                            change the non-bonded parameters to modify
                            the<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;interaction
                            between water molecules and protein
                            molecules.<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp; I am using
                            CHARMM forcefield with Tip3p water.<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp; The
                            ffnonbonded.itp file of the forcefield has
                            non-bonded<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;parameters for
                            tip3p water. Can I achieve the above by
                            changing<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;these
                            parameters?<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp; <br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp;That depends on
                            your definition of "modify," but yes, in a
                            way, you<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp;can make changes
                            here. <br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; 1) Modify - Multiply
                            sigma and epsilon by a constant<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;If yes, will
                            this also change the non-bonded parameters
                            for<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp; &nbsp; &nbsp; &nbsp;water - water
                            interaction?<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font><br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>2) Is there a way to
                            add a new ifdef perhaps such that a modified
                            sigma and epsilon can be used for
                            water-protein interactions and the
                            unmodified parameters can be used for
                            water-water interactions?<br>
                            <font style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);"><font
                                style="font-weight: normal; font-size:
                                14px; font-style: normal;
                                background-color: rgb(245, 248, 240);">&gt;
                              </font>&gt; </font>&nbsp;<br>
                          </blockquote>
                          <font style="font-weight: normal; font-size:
                            14px; font-style: normal; background-color:
                            rgb(245, 248, 240);"><font
                              style="font-weight: normal; font-size:
                              14px; font-style: normal;
                              background-color: rgb(245, 248, 240);">&gt;
                            </font>&gt; </font><br>
                        </div>
                        <font style="font-weight: normal; font-size:
                          14px; font-style: normal; background-color:
                          rgb(245, 248, 240);"><font style="font-weight:
                            normal; font-size: 14px; font-style: normal;
                            background-color: rgb(245, 248, 240);">&gt;
                          </font>&gt; </font>Nonbonded interactions are
                        calculated during the simulation by applying the
                        combination rules defined by the force field.
                        &nbsp;There is no simple way to do this with an
                        ifdef, since that is just in the topology. &nbsp;You
                        can't conditionally apply nonbonded parameters.
                        &nbsp;That just sounds like a recipe for breaking a
                        force field.<br>
                      </blockquote>
                    </div>
                    <font style="font-weight: normal; font-size: 14px;
                      font-style: normal; background-color: rgb(245,
                      248, 240);">&gt; </font><br>
                  </div>
                  <font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font>Not quite right. Parameters for
                  VDW are calculated from the combination rules from the
                  atom-specific values given in [atomtypes] only as a
                  last resort. [nonbond_params] are used in preference
                  to such.<br>
                  <font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font><br>
                  <font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font>So modified protein-water VDW
                  interactions can be introduced by defining all
                  relevant "protein atom"-"TIP3P oxygen"
                  [nonbond_params] terms. It may be simpler to modify
                  the [atomtypes] to generate the "modified" VDW from
                  the combination rule, and introduce the "normal" TIP3P
                  oxygen-oxygen interaction via [nonbond_params].<br>
                </blockquote>
                <div><font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font>&nbsp;</div>
                <div><font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font>Mark, could you please elaborate
                  the method?</div>
                <blockquote class="gmail_quote" style="padding-left:
                  1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid
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                  <font style="font-weight: normal; font-size: 14px;
                    font-style: normal; background-color: rgb(245, 248,
                    240);">&gt; </font>--<br>
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      <br>
      -- <br>
      Quaerendo Invenietis-Seek and you shall discover.<br>
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