Regarding my previous question. I performed 2 simulations (minimization, NVT, NPT, and that 10ns production run), one with 300K and another with 309K. Fir each temperature I calculated how many contacts has my molecule with water within a certain distance. But the number of contacts at different temperatures is the same. It differs on 0.1. I think it has something to do with pressure. I would really like to be able to perform simulations that I could get correct different value of number of contacts versus temperature. <br>
<br>Please could you advice me on this?<br><br>best,<br>Olga<br><br><div class="gmail_quote">2011/2/23 Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Olga Ivchenko wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes, I want to plot number of contacts agains tempreture. But in thermodynamics when temperature changes the pressure changes or the volume. But in my system volume and pressure is the same at different tempretures. Just I wanted ti be sure if it is ok to do like this even if the pressure is the same at different tempretures.<br>

<br>
</blockquote>
<br></div>
I guess this all depends on how &quot;different&quot; your temperatures are.  If the pressures do not change substantially, then there is no problem, since the system density is reasonably similar.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
best,<br>
Olga<br>
<br>
2011/2/23 Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<div class="im"><br>
<br>
<br>
<br>
    Olga Ivchenko wrote:<br>
<br>
        If I am using g_mindist to calculate the number of contacts at<br>
        different tempretures of the system. I am thinking if it will<br>
        make sense because the system has a periodic boundary conditions<br>
        and the pressure at each tempreture is defined manually and is<br>
        the same. The only parameter in the script which should be<br>
        different at different tempretures is pressure. Please could you<br>
        advice me on this?<br>
<br>
<br>
    So you want to plot contacts as a function of temperature?  I don&#39;t<br>
    see any problem with doing that.  On what do you need advice?<br>
<br>
    -Justin<br>
<br>
        best,<br>
        Olga<br>
<br>
        2011/2/21 Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt; &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;<br>
<br>
<br>
<br><div><div></div><div class="h5">
           Olga Ivchenko wrote:<br>
<br>
               So I used mindist for a certain group of molecules which is<br>
               surrounded by water. I got plot number of contacts versuc<br>
               sumulation time. According to what I see in a distance  &lt;<br>
        0.6nm<br>
               at certain frame there are on average 150 contacts.<br>
<br>
               Actually how the programm calculates the number of<br>
        contacts, if<br>
               someone knows what is a creteria that a certain contact<br>
        is formed?<br>
               Is is a certain distance.<br>
<br>
<br>
           Exactly as the title of the output says, a contact exists if<br>
        any two<br>
           atoms of the chosen index groups are within 0.6 nm.  You can<br>
        change<br>
           the distance with g_mindist -d.<br>
<br>
           -Justin<br>
<br>
               best,<br>
               Olga<br>
<br>
               2011/2/21 Olga Ivchenko &lt;<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a><br>
        &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a>&gt;<br>
               &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a><br>
        &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a>&gt;&gt;<br>
        &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a> &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a>&gt;<br>
<br>
               &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a><br>
        &lt;mailto:<a href="mailto:olga.ivchenko@gmail.com" target="_blank">olga.ivchenko@gmail.com</a>&gt;&gt;&gt;&gt;<br>
<br>
<br>
                  Thank you very much.<br>
                  best,<br>
                  Olga<br>
<br>
                  2011/2/21 Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
<br></div></div>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt;<div><div></div><div class="h5">
<br>
<br>
<br>
<br>
                      g_mindist -on (with suitable index groups) should<br>
        also do<br>
               the trick.<br>
<br>
                      -Justin<br>
<br>
<br>
                      Erik Marklund wrote:<br>
<br>
                          Or g_hbond -contact. Undfortuntely there are<br>
        still issues<br>
                          with g_hbond at the moment. Version 4.0.x seem to<br>
               work better.<br>
<br>
                          XAvier Periole skrev 2011-02-21 11.37:<br>
<br>
                              g_dist<br>
                              On Feb 21, 2011, at 11:32 AM, Olga<br>
        Ivchenko wrote:<br>
<br>
                                  Dear Gromacs Users,<br>
<br>
                                  I would like to know if there is in<br>
        gromacs an<br>
                                  option how to calculate how many<br>
        contacts has a<br>
                                  certain atom i(n a molecules of interest)<br>
               with water<br>
                                  during the whole MD simulations (or at<br>
        each<br>
               step of MD).<br>
                                  Please could you advice me on this?<br>
<br>
                                  best,<br>
                                  Olga<br>
<br>
                                  --                     gmx-users<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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