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<p class="MsoNormal">Greetings all,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Background:</p>
<p class="MsoNormal">I have a series of MD runs of a protein ligand complex where I have used PME, they represent far more calculations than I have time to repeat in full. I recently became aware that the
<span class="SpellE">coulombic</span> interaction energy reported when PME is used is not valid for use with
<span class="SpellE">g_lie</span> (or any LIE method). I have read some relevant LIE papers and it seems that reaction field is the electrostatic method used.</p>
<p class="MsoNormal"><a href="http://pubs.acs.org/doi/abs/10.1021/jm7012198" target="_blank">http://pubs.acs.org/doi/abs/10.1021/jm7012198</a></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Current methodology: </p>
<p class="MsoNormal">I found that using <span class="SpellE">mdrun</span> –rerun and a new .<span class="SpellE">tpr</span> file I can change reported energies. Are these energies corresponding to the settings in the new .<span class="SpellE">mdp</span> file?
Can I change it from PME to Generalised-Reaction-Field? Are there any errors associated with changing it, as opposed to errors implicit in either method? I am understanding –rerun to only be calculated for the co-ordinate frames that are outputted into the
.<span class="SpellE">xtc</span> file irrespective of any settings in the new .<span class="SpellE">mdp</span> file and/or old .<span class="SpellE">mdp</span> file for the energy.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">As I only outputted .<span class="SpellE">xtc</span> files I don’t have velocities (or did I set that in the .<span class="SpellE">mdp</span> file?)
<span style=""> </span>but I assume that errors in kinetic energy, temperature and pressure are not important in the rerun as I am only concerned with interaction energy?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Right assuming all the above is valid I would like to improve my accuracy as much as possible.</p>
<p class="MsoNormal">My understanding of cut offs is that the bigger they are the more accurate and the more computationally expensive your calculations are until they approach half the shortest box vector where
<span class="SpellE">pbc</span> issues cause errors. As I am only doing reruns now I should use the largest possible cut offs that don’t hit the
<span class="SpellE">pbc</span> limit? </p>
<p class="MsoNormal">Is there an accuracy difference between the short range and long range calculations for the LJ potential? (is there a reason to use long range at all?)
</p>
<p class="MsoNormal">For the reruns can I ignore the problem of a water molecule seeing both sides of my protein and use a cut off greater than the editconf -d setting (in my case 1.6)? Or to be strictly accurate should I work out the distance to the other
side of the mirror protein from the binding site via the pbc boundary and use half that?</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">Which brings me to my issue with the unit cell. I set -bt dodecahedron. But I don't see it as one (vmd/pymol display of water atoms/unit cell). How do I relate the vectors in the.gro file to the pbc arrangement?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">------------------------------------</p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">2584CL<span style="">
</span>CL 7792<span style=""> </span>5.230<span style=""> </span>2.213<span style="">
</span>3.017<span style=""> </span>0.0075<span style=""> </span>0.3566<span style="">
</span>0.5809</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">2585CL<span style="">
</span>CL 7793<span style=""> </span>1.448<span style=""> </span>2.710<span style="">
</span>1.489<span style=""> </span>0.5771<span style=""> </span>0.2054<span style="">
</span>0.0146</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">2586CL<span style="">
</span>CL 7794<span style=""> </span>3.070<span style=""> </span>1.270<span style="">
</span>3.024 -0.1756 -0.0490 -0.1351</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">2587CL<span style="">
</span>CL 7795<span style=""> </span>5.112<span style=""> </span>2.558<span style="">
</span>1.562 -0.1543 -0.0592 -0.0072</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">2588CL<span style="">
</span>CL 7796<span style=""> </span>2.906<span style=""> </span>1.133<span style="">
</span>1.094 -0.2265 -0.3952<span style=""> </span>0.1190</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New""><span style="">
</span>4.80953<span style=""> </span><span class="SpellE">4.80953</span><span style="">
</span>3.40085<span style=""> </span>0.00000<span style=""> </span><span class="SpellE">0.00000</span><span style="">
</span><span class="SpellE">0.00000</span><span style=""> </span><span class="SpellE">0.00000</span><span style="">
</span>2.40476<span style=""> </span><span class="SpellE">2.40476</span></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New"">----------------------</span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt; font-family:"Courier New""> </span></p>
<p class="MsoNormal" style="text-autospace:none">In my trials I got the error</p>
<p class="MsoNormal">“ERROR 1 [file <span class="SpellE">topol.top</span>, line 50]:</p>
<p class="MsoNormal"><span style=""> </span>ERROR: The cut-off length is longer than half the shortest box vector or</p>
<p class="MsoNormal"><span style=""> </span>longer than the smallest box diagonal element. Increase the box size or</p>
<p class="MsoNormal"><span style=""> </span>decrease <span class="SpellE">rlist</span>.”</p>
<p class="MsoNormal">So if I understand the .<span class="SpellE">gro</span> file correctly (now) these vectors are the long diagonals of three rhombuses. Two are at right angles to each other and the third connects two a lower edge on each of those. Trial
and error lead me to the maximum cut off that <span class="SpellE">grompp</span> will accept is 2.40476, which is d/2, if I read this correctly. My question is, why don't my waters and/or unit cell appear to be a dodecahedron when viewed in VMD/pymol? For
that matter why don't the waters and unit cell agree on a shape when viewed in VMD? (both are rhombic prisims).</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">All the best,</p>
<p class="MsoNormal">Tom</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal"> </p>
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