<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">When using softwares like VMD to visualize membranes where lipids exhibit <a href="https://www.steemstem.io/#!/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">interdigitation</a> as in our case, it will very useful if you can sort out those lipids which specifically exhibit this phenomenon. And this task is not straight forward as it seems. But there are neat tricks which you can useto select them. We know that in our case lipid defects initiates interdigitation. See my <a href="https://www.steemstem.io/#!/@dexterdev/visualizing-lipid-de-1549468204" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">previous post</a> for the explanation. Also we know that waters getting trapped in these lipid defects. So the first step is to select those waters. It can be done in VMD as below:</p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll;">(water pbwithin 4 of (lipid and (name C314 C214)))</code></p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">C314 and C214 are the bottom-most carbon atoms from the fatty acid tails of DMPC lipids. We are selecting water within 4 Angstrom of these carbons. Now select the lipid atoms within 4 angstrom of these selections:</p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll;">(lipid pbwithin 4 of (water pbwithin 4 of (lipid and (name C314 C214))))</code></p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">And finally, select the complete fragment(otherwise the selection of lipids will be like broken atoms here and there.)</p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll;">same fragment as (lipid pbwithin 4 of (water pbwithin 4 of (lipid and (name C314 C214))))</code></p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">And now if you want to select the non-interdigitated lipids, just invert the selection:</p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll;">lipid and not (same fragment as (lipid pbwithin 4 of (water pbwithin 4 of (lipid and (name C314 C214)))))</code></p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">See my youtube videos below which illustrates these selections(you can reduce the video speed in youtube settings to see the evolution/emergence of interdigitation clearly):</p>
<p style="margin-bottom: 1.5rem; padding: 0px; line-height: 28.8px; text-rendering: optimizeLegibility; background-color: rgb(252, 252, 252);">https://www.youtube.com/watch?v=StmtHj4gL3A</p>
<p style="margin-bottom: 1.5rem; padding: 0px; line-height: 28.8px; text-rendering: optimizeLegibility; background-color: rgb(252, 252, 252);">https://www.youtube.com/watch?v=W1Xm6AjgeHI</p>
<p style="margin-bottom: 1.5rem; padding: 0px; line-height: 28.8px; text-rendering: optimizeLegibility; background-color: rgb(252, 252, 252);"><span style="color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px;">The blue colored lipids are those in the lipid defect areas, which is beginning to show interdigitation or is exhibiting it. The red region is the non-interdigitated ones(including fluidy lipids/ gel-phase lipids).</span></p>
<p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">Few features of the interdigitated lipids are:</p>
<ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;">They exhibit strong positive correlation in their motion among them. Very sychronized motion among interdigitated lipids!</li><li style="margin: 0px; padding: 0px; font-size: inherit;">There is a phase separation between interdigitated and other lipids.</li></ul>
<p></p><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 26.88px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;">References</h2><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 23.04px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;">My previous posts:</h3><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">To learn about VMD and PDB file format, see here:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-2-introduction-to-tcl-scripting-environment-in-vmd-1-sbd-prize-task-inside" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-2-introduction-to-tcl-scripting-environment-in-vmd-1-sbd-prize-task-inside</a></li></ul><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">To learn about the concepts in All-atom molecular dynamics see articles below:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-1-the-fundamentals" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-1-the-fundamentals</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-2-the-force-field" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-2-the-force-field</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-3-solving-the-molecular-dynamics-equation" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-3-solving-the-molecular-dynamics-equation</a></li></ul><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">To setup and run simulations in NAMD software, see below:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4a-let-us-setup-a-simulation-and-run-it" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4a-let-us-setup-a-simulation-and-run-it</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4b-running-small-systems-on-your-computer" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4b-running-small-systems-on-your-computer</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility</a></li></ul><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 23.04px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;">Textbook references:</h3><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;">"Statistical Mechanics: Theory and Molecular Simulations" by Mark E. Tuckerman</li><li style="margin: 0px; padding: 0px; font-size: inherit;">"Molecular Modelling: Principles and Applications" by Andrew R. Leach</li><li style="margin: 0px; padding: 0px; font-size: inherit;">"Computer Simulation of Liquids" by D. J. Tildesley and M.P. Allen</li><li style="margin: 0px; padding: 0px; font-size: inherit;">"Thermal Biophysics of Membranes" by Thomas Heimburg</li></ul><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 23.04px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;">References specific to NAMD and VMD:</h3><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Research/namd/cvs/ug.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">NAMD userguide</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">NAMD tutorial</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">VMD userguide</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Training/TutorialsOverview/vmd/vmd-tutorial.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">VMD tutorial</a></li></ul><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 26.88px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;"><a href="https://steemit.com/trending/steemstem" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">#steemSTEM</a></h2><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><a href="https://steemit.com/trending/steemstem" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">#steemSTEM</a> is a very vibrant community on top of STEEM blockchain for Science, Technology, Engineering and Mathematics (STEM). 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color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">10000SP</a>).</p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);">Also visit and create your STEM posts using steemstem app here: <a href="https://www.steemstem.io/" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io</a><br>You can also set <a href="https://steemit.com/@steemstem" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">@steemstem</a> as beneficiary.</p><hr style="box-sizing: content-box; overflow: visible; clear: both; max-width: 75rem; margin: 1.25rem auto; border-top: 0px; border-right: 0px; border-left: 0px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238); color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"><span style="font-weight: 600; line-height: inherit;"></span></p><center style="color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><span style="font-weight: 600; line-height: inherit;">All images without image sources are my creations :)</span></center><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"></p><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: rgb(51, 51, 51); text-rendering: optimizeLegibility; font-size: 26.88px; background-color: rgb(252, 252, 252); line-height: 1.2 !important;"><center>Follow me <a href="https://steemit.com/@dexterdev" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">@dexterdev</a></center></h2><hr style="box-sizing: content-box; overflow: visible; clear: both; max-width: 75rem; margin: 1.25rem auto; border-top: 0px; border-right: 0px; border-left: 0px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238); color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; background-color: rgb(252, 252, 252);"></p><center style="color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><pre style="margin-top: 0px; margin-bottom: 0px; padding: 0px;"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll; display: block;"> ____ _______ ______ _________ ____ ______
/ _ / __\ \//__ __/ __/ __/ _ / __/ \ |\
| | \| \ \ / / \ | \ | \/| | \| \ | | //
| |_/| /_ / \ | | | /_| | |_/| /_| \//
\____\____/__/\\ \_/ \____\_/\_\____\____\__/
</code></pre><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: inherit; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;"></h2><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><center><img src="https://steemitimages.com/DQmVM9FmLfAYojdB7Ex2ooGhkZMGHht3NzPLUSEvwSvpjTd/dexter.png" style="border-style: none; display: inline-block; vertical-align: middle; height: auto; width: auto; max-height: none;"><br>credit: <a href="https://steemit.com/@mathowl" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">@mathowl</a></center><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><hr style="box-sizing: content-box; overflow: visible; clear: both; max-width: 75rem; margin: 1.25rem auto; border-top: 0px; border-right: 0px; border-left: 0px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238);"><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Bye now!</p></center><p style="margin-bottom: 1.5rem; padding: 0px; line-height: 28.8px; text-rendering: optimizeLegibility; background-color: rgb(252, 252, 252);"><font color="#333333" face="Source Serif Pro, serif"><span style="font-size: 19.2px;"><br></span></font></p><p></p>
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