<p class="MsoNormal"><span style="color:#222222"><br>
Dear Gromacs Users,<br>
<br>
I am using gromacs version 4.5.5.and running
my jobs on single node with 8 cores. My system contains about
425000 atoms (protein + Lipid +SOL). I have successfully
reached up to Energy minimization step.</span><span style="color:rgb(34,34,34)">As per the suggestion by Dear
Mark, I am starting my NPT equilibration with Berendsen and further with Parinello-Rahman
to get the right ensemble.</span><span style="color:rgb(34,34,34)">But when I am trying for NPT equilibration </span><span style="color:rgb(34,34,34)">with Berendsen</span><span style="color:rgb(34,34,34)">, getting following Warnings.</span></p>
<p class="MsoNormal"><span style="color:#222222"> </span></p><p class="MsoNormal"><span style="font-family:'Times New Roman',serif;font-size:12pt">WARNING
1 [file npt.mdp]: </span><span style="font-family:'Times New Roman',serif;font-size:12pt">Using Berendsen pressure coupling
invalidates the true ensemble for the thermostat</span></p><p class="MsoPlainText"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">WARNING 2 [file npt.mdp]: </span><span style="font-family:'Times New Roman',serif;font-size:12pt">You
are using pressure coupling with absolute position restraints, this will give
artifacts. </span><span style="font-family:'Times New Roman',serif;font-size:12pt"> </span><span style="font-family:'Times New Roman',serif;font-size:12pt">Use the refcoord_scaling
option.</span></p><p class="MsoPlainText"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">
</span><span style="font-size:12pt;font-family:'Times New Roman',serif">And
about 10 such </span><span style="font-family:'Courier New'">LINCS </span><span style="font-size:12pt;font-family:'Times New Roman',serif">warnings while running the job as shown
below:</span></p><p class="MsoPlainText"><span style="font-family:'Courier New'">Step 39, time
0.078 (ps)</span><span style="font-family:'Courier New'"> </span><span style="font-family:'Courier New'">LINCS WARNING</span></p><p class="MsoPlainText"><span style="font-family:'Courier New'">relative constraint deviation after LINCS:</span></p>
<p class="MsoPlainText"><span style="font-family:"Courier New"">
rms 0.000029, max 0.000473 (between atoms 890 and 891)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle
previous, current, constraint length<br>
12050
12049 31.2 0.1000
0.1000 0.1000<br>
11721
11720 46.0 0.1000
0.1000 0.1000<br>
5496
5495 36.8 0.1000
0.1000 0.1000<br>
<br>
</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">
</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif";color:#222222">With
–</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">maxwarn option I
am able to run it, and output density and pressure seems perfectly alright.</span></p>
<p class="MsoNormal">Based on the same I want to know:-</p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoNormal" style="color:#222222"><span style="color:windowtext">How does pressure coupling with Berendsen invalidates
the true ensemble?</span></li>
</ol>
<p class="MsoNormal" style="margin-left:.5in">At least for initial fixing of
density and pressure?</p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222">Whether
to bother for above mentioned warning or ignore it?</span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222"> </span></p>
<ol style="margin-top:0in" start="2" type="1">
<li class="MsoNormal" style="color:#222222"><span style="color:windowtext">Pressure coupling with absolute position
restraints warning how it will lead to artifacts?</span></li>
</ol>
<p class="MsoNormal" style="margin-left:.5in">How one can use refcoord_scaling
option in this situation?</p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222">Whether
to bother for above mentioned warning or ignore it?</span></p>
<ol style="margin-top:0in" start="3" type="1">
<li class="MsoNormal" style="color:#222222">Using <span style="color:windowtext">Berendsen with semiisotropic couple type is wrong
method or no such problem?</span></li>
</ol>
<p class="MsoNormal"><span style="color:#222222"> </span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222">Please suggest
me whether to move ahead with ignorance to the warnings or to change some
parameters in mdp file?</span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222">I have
attached my npt.mdp file for your consideration.</span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222"> </span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="color:#222222">Thanking
you In advance,</span></p><div><br></div><div>Pavan Payghan</div>
<div> </div>
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