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    On 4/23/2011 9:21 AM, majid hasan wrote:
    <blockquote cite="mid:533604.60211.qm@web38307.mail.mud.yahoo.com"
      type="cite">
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        <div style="color: black; font-family: 'times new roman','new
          york',times,serif; font-size: 12pt;">Okay, thanks, I removed
          restraints from water.</div>
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          york',times,serif; font-size: 12pt;"><br>
        </div>
        <div style="color: black; font-family: 'times new roman','new
          york',times,serif; font-size: 12pt;">&nbsp;In the final simulation,
          I increased the simulation time from 20ps to 2000ps to see if
          they wrap around. However in .trr output, CNT and DNA remain
          stable, jiggles around and jump across the box in a weird
          manner (might have something to do with periodic boundary
          conditions?) but don't seem to be attracted towards each
          other.&nbsp;</div>
        <div style="color: black; font-family: 'times new roman','new
          york',times,serif; font-size: 12pt;"><br>
        </div>
        <div style="color: black; font-family: 'times new roman','new
          york',times,serif; font-size: 12pt;">Movie of output is here:</div>
        <div><font class="Apple-style-span" face="'times new roman',
            'new york', times, serif"><span><a moz-do-not-send="true"
                target="_blank"
                href="http://phas.ubc.ca/%7Emajid/Project/msteps/cntdna2000ps.mpg">http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg</a></span></font></div>
        <div><font class="Apple-style-span" face="'times new roman',
            'new york', times, serif">and input em.mdp, and md.mdp files
            are here:</font></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">EM:&nbsp;<a
            moz-do-not-send="true"
            href="http://phas.ubc.ca/%7Emajid/Project/msteps/lbfgs.mdp">http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp</a></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">MD:&nbsp;<a
            moz-do-not-send="true"
            href="http://phas.ubc.ca/%7Emajid/Project/msteps/md.mdp">http://phas.ubc.ca/~majid/Project/msteps/md.mdp</a></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><br>
        </div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">Commands
          that I have been using to build input coordinates, and
          topologies are below:</div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><br>
        </div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><span
            class="Apple-style-span" style="font-family:
            arial,helvetica,sans-serif; font-size: 13px;">&nbsp;For dna: &nbsp; &nbsp;
            &nbsp; &nbsp; &nbsp; pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select
            (Selected amber99sb, and TIP3P water model)<br>
            &nbsp;</span></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><span
            class="Apple-style-span" style="font-family:
            arial,helvetica,sans-serif; font-size: 13px;">For cnt: &nbsp; &nbsp; &nbsp;
            &nbsp; &nbsp; &nbsp; g_x2top -f cnt.gro -o cnt.top -ff select -pbc&nbsp;
            (selected amber99sb)<br>
            &nbsp;</span></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><span
            class="Apple-style-span" style="font-family:
            arial,helvetica,sans-serif; font-size: 13px;">For mixing : &nbsp;
            &nbsp; &nbsp; &nbsp;genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1
            -try 20&nbsp;</span></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><span
            class="Apple-style-span" style="font-family:
            arial,helvetica,sans-serif; font-size: 13px;"><br>
          </span></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><span
            class="Apple-style-span" style="font-family:
            arial,helvetica,sans-serif; font-size: 13px;">For solvation:
            &nbsp; &nbsp;&nbsp;genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro</span></div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;"><br>
        </div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">I have no
          clue what is wrong with the simulation, and any help is much
          appreciated. <br>
        </div>
      </div>
    </blockquote>
    <br>
    You're still not following a sound equilibration protocol. The
    velocities you generate at the start are only roughly correct, and
    your density is probably a bit off. Check out some tutorials, and
    published work on similar systems.<br>
    <br>
    You also need to consider how far apart these species are. If the
    driving force is electrostatic, the forces drop off as 1/r^2, so you
    can wait a long time for those to act over a few nanometers, while
    re-organizing the solvent between them.<br>
    <br>
    In real biochemical systems, one doesn't normally observe a single
    pair of interacting species mate up smoothly. There's a whole pile
    of things that have to happen, and each successful binding probably
    results from very many failed attempts. Having many such pairs over
    longer periods of times means that statistically the events do
    happen, but that's no good to you if you can only simulate a single
    pair in a short period.<br>
    <br>
    Mark<br>
    <br>
    <blockquote cite="mid:533604.60211.qm@web38307.mail.mud.yahoo.com"
      type="cite">
      <div style="font-family: 'times new roman','new york',times,serif;
        font-size: 12pt;">
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">Thanks,</div>
        <div style="font-family: 'times new roman','new
          york',times,serif; font-size: 12pt; color: black;">Majid<br>
          <div style="font-family: arial,helvetica,sans-serif;
            font-size: 10pt;"><font face="Tahoma" size="2">
              <hr size="1"><b><span style="font-weight: bold;">From:</span></b>
              Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu">&lt;jalemkul@vt.edu&gt;</a><br>
              <b><span style="font-weight: bold;">To:</span></b> Gromacs
              Users' List <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a><br>
              <b><span style="font-weight: bold;">Sent:</span></b> Fri,
              April 22, 2011 10:59:22 AM<br>
              <b><span style="font-weight: bold;">Subject:</span></b>
              Re: [gmx-users] DNA not wrapping around CNT in MD
              simulation<br>
            </font><br>
            <br>
            <br>
            majid hasan wrote:<br>
            &gt; Yes, ideally I didn't want to, but I read somewhere on
            mailing list that one shouldn't use define = -DFLEXIBLE
            while running dynamics. So I thought I will use restrained
            water...<br>
            &gt; <br>
            &gt; I'll move back to -DFLEXIBLE though, if I got a
            successful mdrun for restrained water.<br>
            &gt; <br>
            <br>
            Constraints and restraints are separate ideas.<br>
            <br>
            <span><a moz-do-not-send="true" target="_blank"
href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a></span><br>
            <br>
            If you *restrain* the water, the molecules won't move.&nbsp; If
            you *constrain* (i.e., using rigid water and not -DFLEXIBLE,
            which for MD you shouldn't be doing) you fix the geometry of
            a molecule while still allowing it to actually move.<br>
            <br>
            -Justin<br>
            <br>
            &gt; Thanks,<br>
            &gt; Majid<br>
            &gt; <br>
            &gt;
            ------------------------------------------------------------------------<br>
            &gt; *From:* Justin A. Lemkul &lt;<a moz-do-not-send="true"
              ymailto="mailto:jalemkul@vt.edu"
              href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;<br>
            &gt; *To:* Discussion list for GROMACS users &lt;<a
              moz-do-not-send="true"
              ymailto="mailto:gmx-users@gromacs.org"
              href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>
            &gt; *Sent:* Fri, April 22, 2011 10:44:45 AM<br>
            &gt; *Subject:* Re: [gmx-users] DNA not wrapping around CNT
            in MD simulation<br>
            &gt; <br>
            &gt; <br>
            &gt; <br>
            &gt; majid hasan wrote:<br>
            &gt;&nbsp; &gt; I just checked and DNA position should not be
            restrained because I didn't use define = -DPOSRES in .mdp
            file. I am going to run it for a longer time now, and use
            position restraints for water<br>
            &gt;&nbsp; &gt;<br>
            &gt; <br>
            &gt; What purpose does restraining the water have?&nbsp; You'll
            be trying to observe diffusion of your DNA or CNT through an
            immobile solvent.<br>
            &gt; <br>
            &gt; -Justin<br>
            &gt; <br>
            &gt;&nbsp; &gt; Thank You,<br>
            &gt;&nbsp; &gt; Majid.<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt;
            ------------------------------------------------------------------------<br>
            &gt;&nbsp; &gt; *From:* Mark Abraham &lt;<a
              moz-do-not-send="true"
              ymailto="mailto:Mark.Abraham@anu.edu.au"
              href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>
            &lt;mailto:<a moz-do-not-send="true"
              ymailto="mailto:Mark.Abraham@anu.edu.au"
              href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;&gt;<br>
            &gt;&nbsp; &gt; *To:* Discussion list for GROMACS users &lt;<a
              moz-do-not-send="true"
              ymailto="mailto:gmx-users@gromacs.org"
              href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
            &lt;mailto:<a moz-do-not-send="true"
              ymailto="mailto:gmx-users@gromacs.org"
              href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;&gt;<br>
            &gt;&nbsp; &gt; *Sent:* Fri, April 22, 2011 1:51:47 AM<br>
            &gt;&nbsp; &gt; *Subject:* Re: [gmx-users] DNA not wrapping
            around CNT in MD simulation<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt; On 4/22/2011 6:48 PM, Mark Abraham wrote:<br>
            &gt;&nbsp; &gt;&gt; On 4/22/2011 4:54 PM, majid hasan wrote:<br>
            &gt;&nbsp; &gt;&gt;&gt; Dear All,<br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt; I am doing a MD simulation of dna, and
            cnt in water. I get a stable simulation in which DNA, and
            CNT wiggles around there positions, but they don't seem to
            be attracted towards each other. CNT starts in the middle of
            the box and just moves a little, and DNA starts at top right
            corner of the box and remains there throughout the
            simulation.<br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt; movie of .trr file is here:<br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            <span>&gt;&gt; &gt;&gt; <a moz-do-not-send="true"
                target="_blank"
                href="http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg">http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg</a></span><br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt; My .mdp files are placed here (both .mdp
            files are same except for the value of integrator):<br>
            <span>&gt;&gt; &gt;&gt; <a moz-do-not-send="true"
                target="_blank"
                href="http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp">http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp</a>&nbsp;
              (used for EM)</span><br>
            <span>&gt;&gt; &gt;&gt; <a moz-do-not-send="true"
                target="_blank"
                href="http://phas.ubc.ca/%7Emajid/Project/md.mdp">http://phas.ubc.ca/%7Emajid/Project/md.mdp</a>&nbsp;
              &nbsp; (used for MD)</span><br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt; I created cnt, and dna using following
            commands:<br>
            &gt;&nbsp; &gt;&gt;&gt; For dna: pdb2gmx -f dna.pdb -o dna.gro -p
            dna.top -ff select (Selected amber99sb, and TIP3P water
            model)<br>
            &gt;&nbsp; &gt;&gt;&gt; For cnt: g_x2top -f cnt.gro -o cnt.top
            -ff select -pbc&nbsp; (selected amber99sb)<br>
            &gt;&nbsp; &gt;&gt;&gt; For mixing and solvation: genbox -cp
            cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp
            cntdna.gro -cs spc.gro -o cntdnasol.gro<br>
            &gt;&nbsp; &gt;&gt;&gt; In the dna.top file, amber99sb/ions.itp,
            and a position restraint file was also included along with
            tip3p.itp. I mentioned it because I am not sure why would it
            add ions and position restraints on adding water?<br>
            &gt;&nbsp; &gt;&gt;<br>
            &gt;&nbsp; &gt;&gt; #including molecule .itp files adds nothing
            to the system - only the potential to have molecule type(s).
            The system is defined in the [system] directive, and must
            match the corresponding coordinate file.<br>
            &gt;&nbsp; &gt;&gt;<br>
            &gt;&nbsp; &gt;&gt;&gt; It seems that something is wrong with
            non-bonded interactions, but I don't understand what?<br>
            &gt;&nbsp; &gt;&gt;<br>
            &gt;&nbsp; &gt;&gt; Why aren't you following a proper
            equilibration protocol before trying to make observations?
            You might be using position restraints, have your species
            too far apart, or simply have not simulated long enough to
            observe any movement. 200ps is an eye-blink.<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt; Actually, you simulated 20ps. Your MD timestep is
            0.2fs, which is unreasonably short. 100,000 of them is far
            too short to see anything happen.<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt; Mark<br>
            &gt;&nbsp; &gt;<br>
            &gt; <br>
            &gt; -- ========================================<br>
            &gt; <br>
            &gt; Justin A. Lemkul<br>
            &gt; Ph.D. Candidate<br>
            &gt; ICTAS Doctoral Scholar<br>
            &gt; MILES-IGERT Trainee<br>
            &gt; Department of Biochemistry<br>
            &gt; Virginia Tech<br>
            &gt; Blacksburg, VA<br>
            &gt; jalemkul[at]<a moz-do-not-send="true" target="_blank"
              href="http://vt.edu">vt.edu</a><span> &lt;<a
                moz-do-not-send="true" target="_blank"
                href="http://vt.edu">http://vt.edu</a>&gt; | (540)
              231-9080</span><br>
            <span>&gt; <a moz-do-not-send="true" target="_blank"
                href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br>
            &gt; <br>
            &gt; ========================================<br>
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            -- ========================================<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]vt.edu | (540) 231-9080<br>
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