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    On 3/08/2011 2:23 PM, Sanku M wrote:
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        <div style="font-family:times new roman, new york, times,
          serif;font-size:12pt">&nbsp; &nbsp; Finally, I achieved the desired 300K
          average temperature using sd integrator . I had to reduce the
          time step from 0.002 ps to 0.001 ps and then running the NVT
          could produce 300K as average temperature.</div>
        <div style="font-family:times new roman, new york, times,
          serif;font-size:12pt">Still Not sure why md integrator still
          could 300K average temperature using 0.002 ps as time-step.</div>
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    </blockquote>
    <br>
    So your integration step was too large to conserve energy. There
    have been two suggestions made about why that might be true. Have
    you investigated them?<br>
    <br>
    Mark<br>
    <br>
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              <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>
              Discussion list for GROMACS users
              <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> Tue,
              August 2, 2011 10:16:17 PM<br>
              <b><span style="font-weight: bold;">Subject:</span></b>
              Re: [gmx-users] Problem with temperature and stochastic
              dynamics in FEP<br>
            </font><br>
            <br>
            <br>
            Sanku M wrote:<br>
            &gt; Hi Justin,<br>
            &gt;&nbsp; &nbsp; I did calculate the average temperature using last 2
            ns of the 8ns data. It is still same 303K. <br>
            &gt; <br>
            <br>
            Going back to the original .mdp file, I can see that you're
            using some incorrect settings.&nbsp; You've set rlist=rvdw even
            though you're using a shifted potential for van der Waals
            interactions.&nbsp; Surely grompp should have warned you that
            this would lead to poor energy conservation.&nbsp; Your solvent
            is probably heating up as a result and leading to the
            incorrect temperature.<br>
            <br>
            -Justin<br>
            <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:* Tue, August 2, 2011 9:55:40 PM<br>
            &gt; *Subject:* Re: [gmx-users] Problem with temperature and
            stochastic dynamics in FEP<br>
            &gt; <br>
            &gt; <br>
            &gt; <br>
            &gt; Sanku M wrote:<br>
            &gt;&nbsp; &gt; OKK, But, before, I have tried using md as
            integrator where I start the initial velocity as 280K (
            which makes sense as the minimized configuration is
            essentially at low temperature) and have used Nose-hoover at
            300K and I never had problem in getting the desired 300K
            after running a short NVT simulation as equilabration.<br>
            &gt;&nbsp; &gt; The problem arises when sd integrator is used.<br>
            &gt;&nbsp; &gt; In fact, I&nbsp; just tried to generate the initial
            velocity at 300K along with sd integrator. I got the 303 K
            as average temperature again. The same simulation using md
            integrator always gives rise to 300K as average temperature(
            when used in conjunction with Nose-Hoover ) , even if I
            generate velocity at 280 K or 300K .<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt; I guess that the initial velocity-generation
            temperature should not be an issue here. The sd integrator
            in contrast to md integrator may be the problem.<br>
            &gt;&nbsp; &gt;<br>
            &gt;&nbsp; &gt;<br>
            &gt; <br>
            &gt; I have never had such a problem when using sd.&nbsp; I can
            always achieve the target temperature within 0.5 K, if not
            exactly, so I do not believe there is an inherent problem
            with sd.&nbsp; Your first post indicated that your statistics
            were collected over the entire timeframe, which will not be
            correct for reasons I have already described.&nbsp; The initial
            frames will represent unequilibrated data that may skew the
            averages.&nbsp; What if you analyze only the last half of the
            time?&nbsp; The last 1 ns?<br>
            &gt; <br>
            &gt; -Justin<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]vt.edu | (540) 231-9080<br>
            &gt; <a moz-do-not-send="true"
              href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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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>
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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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