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<p class="MsoNormal">Dear all<br>
<br>
I have the following system:<br>
<br>
Two substrates (which are FCC lattices consisting of LJ particles) in a
distance of 50nm and between these substrates I put completely stretched
polymer chains. The substrates are parallel to xy plane and the chains are
vertical. The length of the stretched chains is 30 nm and I put them in the
middle, so the distance of the each substrate to be 10nm. <span style=""> </span>The interaction between the substrates and the
polymers is repulsive and it’s the same for each substrate.</p>
<p class="MsoNormal">I want my substrates to be stable during the simulation, but
to be able also to move under compression (in the z axis). </p>
<p class="MsoNormal">For that purpose in my .mdp file I define the following:</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>nstcomm<span style=""> </span>= 1</b></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>comm-grps<span style=""> </span>= ZZZ<span style=""> </span></b><span style=""></span><i>,where ZZZ is the name of the residue of the
substrates</i></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"><b><i> </i></b></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">I have 2
problems:</p>
<p class="MsoListParagraphCxSpFirst" style="margin-bottom: 0.0001pt; text-indent: -0.25in;"><span style=""><span style="">1)<span style="font: 7pt "Times New Roman";">
</span></span></span>At the beginning, I run NVT for 20ns and the
chains are moving UP during the simulation.</p>
<p class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt;">Since my system is completely symmetric, I would
expect to have symmetric movement of the chains, i.e. symmetric density
profile. <br></p><p class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt;"><span style=""> </span></p>
<p class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt; text-indent: -0.25in;"><span style=""><span style="">2)<span style="font: 7pt "Times New Roman";">
</span></span></span>In my .log file the following message appears:</p>
<p class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt;"><i>Large VCM(group rest):<span style=""> </span>0.00000,<span style=""> </span>-0.00000,<span style=""> </span>0.00001, T-cm:<span style=""> </span>inf</i></p>
<p class="MsoListParagraphCxSpLast" style="margin-bottom: 0.0001pt;">It doesn’t appear as an error message, but it appears
thousand times in my log file. I had a look in the mailing list about that, but
I did not find a proper answer.</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">Can anyone
help me?</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">I also have
one question:</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">When I
remove that COM motion of one residue, i.e. from the ZZZ (by adding comm grps:
ZZZ in my mdp file), what happening with the COM motion of the rest of the
system?</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">I hope I was
clear!</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;">Thanks in
advance, Chrysostomos</p>