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On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote:
<blockquote
cite="mid:CAJ0xtdEW1DjHvnMeUHfNXKpWFHw3+f=5tTAzORZSo1BwYq_7jg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
See manual sections for T and P coupling for introductory
discussion.<br>
<br>
<blockquote
cite="mid:CAJ0xtdEW1DjHvnMeUHfNXKpWFHw3+f=5tTAzORZSo1BwYq_7jg@mail.gmail.com"
type="cite">
<ol style="margin-top:0in" start="1" type="1">
</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>
</blockquote>
<br>
Since you're going to do more equilibration after this, you be the
judge.<br>
<br>
<blockquote
cite="mid:CAJ0xtdEW1DjHvnMeUHfNXKpWFHw3+f=5tTAzORZSo1BwYq_7jg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
See manual.<br>
<br>
<blockquote
cite="mid:CAJ0xtdEW1DjHvnMeUHfNXKpWFHw3+f=5tTAzORZSo1BwYq_7jg@mail.gmail.com"
type="cite">
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#222222">Whether
to bother for above mentioned warning or ignore it?</span></p>
</blockquote>
<br>
Position restraints and NPT is messy. Choose your poison.<br>
<br>
<blockquote
cite="mid:CAJ0xtdEW1DjHvnMeUHfNXKpWFHw3+f=5tTAzORZSo1BwYq_7jg@mail.gmail.com"
type="cite">
<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><br>
</p>
</blockquote>
<br>
That's your judgement to make. How does your preparation protocol
compare to the ones you have read about in the recent literature?<br>
<br>
Mark<br>
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