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<span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: black; FONT-SIZE: 12pt" lang="EN">Dear All,
</span></p>
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<span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: black; FONT-SIZE: 12pt" lang="EN">About the Lincs warnings in Christoph Meier’ problem, is there any improved method or a better way to deal with them? What we can do is to use shorter timesteps or re-start
the simulation using a frame before the first lincs warning?</span><span style="FONT-FAMILY: 'Arial','sans-serif'; COLOR: #888888; FONT-SIZE: 10pt" lang="EN-US"></span></p>
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<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><b><span style="FONT-FAMILY: 宋体; FONT-SIZE: 24pt" lang="EN-US">[gmx-users] LINCS Warnings in the middle of an MD run</span></b></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><b><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">K.A.Feenstra</span></b><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">
<a title="[gmx-users] LINCS Warnings in the middle of an MD run" href="mailto:gmx-users%40gromacs.org?Subject=%5Bgmx-users%5D%20LINCS%20Warnings%20in%20the%20middle%20of%20an%20MD%20run&In-Reply-To=">
<span style="COLOR: blue">k.a.feenstra at chem.rug.nl </span></a><br>
<i>Fri Dec 14 10:49:40 CET 2001</i> </span></p>
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<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">Christoph Meier wrote:</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i>
</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> Dear all,</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i>
</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> One of my GROMACS MD simulations crashed after running stably for almost 4ns (=several</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> weeks on our system). The error message I get is this:</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i>
</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> "...</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> LINCS WARNING</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> relative constraint deviation after LINCS:</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> max 0.000987 (between atoms 3286 and 3289) rms 0.000026</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> bonds that rotated more than 30 degrees:</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i><span>
</span>atom 1 atom 2<span> </span>angle<span> </span>previous, current, constraint length</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> ..."</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i>
</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> I got almost 100 of these LINCS WARNINGs before the system eventually crashed.</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> The atoms involved (3286 and 3289) belong to a protonated lysine residue, the topology</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> of which was generated in the standard (pdb2gmx) way.</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> Does anybody have suggestions as to what I could do to get round this problem ?</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> Do you think there is anything wrong with the lysine residue or anything else ?</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i>
</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">><i> I would be grateful for any advice you could give me. Thanks very much !</i></span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">[.. after reading David's comment, I felt I could add something more...]</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">This is a 'normal' error, in the sense that a rotatable group like</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">your protonated NH3 group in the lysine sidechain, can build up a large</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">rotational velocity. Since this motion couples only weakly with the</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">rest of the system, once you have the high rot. velocity, it stays there</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">for some time. If the velocity builds up too high, lincs will get problems</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">re-setting the bond lengths that get elongeted due to centripetal forces.</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">There is a finite chance to get this buil-up, which obviously increases</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">with simulation length...</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">In short, my view is that this is a more or less physical phenomenon</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">(i.e. not a simulation artefact), but the problem is that eventually at</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">very high velocities your timestep is actually too large. The workaround</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">I usually take is to re-start the simulation using a frame a few 10's of</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">ps before the first lincs warning, and introduce slight round-off errors</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">by using only 6 decimal places (in stead of 7 which are the full precision).
</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">This works as follows:</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">1) use trjconv to write out one frame from your .trr as a .gro file, and</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>set -ndec 6 for the number of decimal places, lile:</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>trjconv -f traj.trr -dump 3890 -o frame.gro -ndec 6</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">2) use trjconv to convert the .gro file back to .trr:</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>trjconv -f frame.gro -o frame.trr</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>(this is because tpbconv will only read from a .trr file)</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">3) use tpbconv to generate a .tpr file with the coordinates/velocities</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>from the selected frame:</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>tpconv -s topol.tpr -f frame.trr -o tpxout.tpr</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span>
</span>you might want to tune the remaining run-time using the -extend option.</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">4) re-start mdrun using tpxout.tpr</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">This trick works because the slight round-off you introduce (6 vs the 7</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">decimal places in a full precision .trr) will cause the simulation to</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">'veer' off its original path very slightly (not normally noticable), with</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">a good chance of avoiding the problematic velocity build-up.</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">--
</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">Groetjes,</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"></span> </p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US">Anton</span></p>
<p style="TEXT-ALIGN: left; MARGIN: 0cm 0cm 0pt" class="MsoNormal" align="left"><span style="FONT-FAMILY: 宋体; FONT-SIZE: 12pt" lang="EN-US"><span> </span>_____________ _____________________________________________________</span></p>
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