<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[RSS Feed]]></title><description><![CDATA[RSS Feed]]></description><link>https://ecency.com</link><image><url>https://ecency.com/logo512.png</url><title>RSS Feed</title><link>https://ecency.com</link></image><generator>RSS for Node</generator><lastBuildDate>Wed, 12 Aug 2026 12:50:04 GMT</lastBuildDate><atom:link href="https://ecency.com/created/molecular-dynamics/rss.xml" rel="self" type="application/rss+xml"/><item><title><![CDATA[COOKE-DESERNO membrane patch forming cylinder!]]></title><description><![CDATA[This is a simulation I am currently doing. The model is described here:]]></description><link>https://ecency.com/@dexterdev/cooke-deserno-membrane-patch-forming-cylinder</link><guid isPermaLink="true">https://ecency.com/@dexterdev/cooke-deserno-membrane-patch-forming-cylinder</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Tue, 09 Feb 2021 10:21:00 GMT</pubDate><enclosure url="https://i.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dvfJKFz1UAJBcCJN7eU9QbGnPsZD9dgSJYe?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Creating a CG vesicle structure and coordinate file for simulations]]></title><description><![CDATA[Hello friends! I am back with my coarse-grained(CG) molecular dynamics(MD) simulation series. Today we will see how to create a vesicle coordinate file and assign it proper topology and structure information.]]></description><link>https://ecency.com/@dexterdev/creating-a-cg-vesicle-structure-and-coordinate-file-for-simulations</link><guid isPermaLink="true">https://ecency.com/@dexterdev/creating-a-cg-vesicle-structure-and-coordinate-file-for-simulations</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 01 May 2020 16:08:51 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnL5gmsP735dBGPpq?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Modelling a "water-free" coarse-grained lipid system]]></title><description><![CDATA[In the last article, we saw how to set-up a coarse-grained simulation using LAMMPS software. In today's article, I will discuss how to come up with a model to simulate a coarse-grained lipid system. In]]></description><link>https://ecency.com/@dexterdev/modelling-a-water-fr-1587907199</link><guid isPermaLink="true">https://ecency.com/@dexterdev/modelling-a-water-fr-1587907199</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 26 Apr 2020 13:20:00 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnLsCPQGfXPD4bfxS?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Longer run of the LAMMPS code from previous post exhibits bilayer self assembly !]]></title><description><![CDATA[I just wanted to update you guys with a longer run of LAMMPS code in my previous article. In my previous article, it seemed that we were observing micelle like structures. But on running it for a longer]]></description><link>https://ecency.com/@dexterdev/longer-run-of-the-la-1586775972</link><guid isPermaLink="true">https://ecency.com/@dexterdev/longer-run-of-the-la-1586775972</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 13 Apr 2020 11:06:15 GMT</pubDate><enclosure url="https://i.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45eQpnxGXuo9uSdwroFtmdLZLB4mGfKeDH3Kk?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A toy example of molecule aggregation to familiarize with LAMMPS software]]></title><description><![CDATA[Hello friends... Welcome to my new molecular dynamics post. As I mentioned in my previous post, I am going to start the new series on coarse-grained lipid models. As an opening article to this series,]]></description><link>https://ecency.com/@dexterdev/a-toy-example-of-molecule-aggregation-to-familiarize-with-lammps-software</link><guid isPermaLink="true">https://ecency.com/@dexterdev/a-toy-example-of-molecule-aggregation-to-familiarize-with-lammps-software</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 06 Apr 2020 10:45:09 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnAgcd4mpTTNinFhg?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A discord server for Biophysics learning and discussions!]]></title><description><![CDATA[Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document the results in the form of HIVE blogs(under]]></description><link>https://ecency.com/@dexterdev/a-discord-server-for-1585836955</link><guid isPermaLink="true">https://ecency.com/@dexterdev/a-discord-server-for-1585836955</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Thu, 02 Apr 2020 14:15:57 GMT</pubDate></item><item><title><![CDATA[Coarse-grained lipid membranes: A teaser of upcoming MD simulation stuff!]]></title><description><![CDATA[Hi friends... To be honest I am overwhelmed with many things recently. And few days back my tinkering became official work(Well... Kinda). Few of you might have seen my previous post. So I will elaborate]]></description><link>https://ecency.com/@dexterdev/coarse-grained-lipid-1585721239</link><guid isPermaLink="true">https://ecency.com/@dexterdev/coarse-grained-lipid-1585721239</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 01 Apr 2020 06:07:21 GMT</pubDate><enclosure url="https://i.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45e4ixpYiUgcHWQmBFFFwp4rnXEh6JTpHzfDG?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Reproduction of a coarse-grained MD paper: A nanoparticle-lipid membrane interaction]]></title><description><![CDATA[This is a reproduction of the Hongyan Yuan et al paper "One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes".The simulation was done in LAMMPS and the parameter]]></description><link>https://ecency.com/@dexterdev/reproduction-of-a-co-1563975484</link><guid isPermaLink="true">https://ecency.com/@dexterdev/reproduction-of-a-co-1563975484</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 24 Jul 2019 13:41:42 GMT</pubDate><enclosure url="https://i.ecency.com/p/3W72119s5BjWMGm4Xa2MvD5AT2bJsSA8F9WeC6rcqfGXTVuNZGUDHYaLp3h86MDEaT6XaoV9qF6DQbvvgjyoyHjqEgmq7FaNJYeKpA4MVFHD4hNFonAxaz?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Our new paper got published in the journal of membrane biology!]]></title><description><![CDATA[![]( Hello Friends! Our new paper got accepted. It's my second paper. The link to the paper is below: Unfortunately, it is behind the SPRINGER paywall! I should write a summary of the paper soon here at]]></description><link>https://ecency.com/@dexterdev/our-new-paper-got-published-in-the-journal-of-membrane-biology</link><guid isPermaLink="true">https://ecency.com/@dexterdev/our-new-paper-got-published-in-the-journal-of-membrane-biology</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 12 Jun 2019 08:46:30 GMT</pubDate><enclosure url="https://i.ecency.com/p/368La1qZAv72Son36dmW5oqyuWGLPdgLW5RoKf3yfKY69V6hGyh8cgWqbeMVfJK4Kq4ux4fHv3gs7DEYt8irz4KF?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Particle in a Double well potential: A molecular dynamics toy example using openMM toolkit]]></title><description><![CDATA[In my previous articles, we have seen many examples which demonstrated classical molecular dynamics simulations of bigger systems likeProtein complex in water boxA lipid bilayer patch system in water]]></description><link>https://ecency.com/@dexterdev/particle-in-a-double-1554311912</link><guid isPermaLink="true">https://ecency.com/@dexterdev/particle-in-a-double-1554311912</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 03 Apr 2019 17:21:48 GMT</pubDate><enclosure url="https://i.ecency.com/0x0/https://i.imgur.com/FizKy8z.gif" length="0" type="image/gif"/></item><item><title><![CDATA[My next Molecular Dynamics Workshop]]></title><description><![CDATA[The day after tomorrow, the Free energy calculations for chemical and biological systems workshopwill begin at IIT, Kanpur. I have got selected for it! And I am very excited to learn new stuff]]></description><link>https://ecency.com/@dexterdev/my-next-molecular-dy-1552651922</link><guid isPermaLink="true">https://ecency.com/@dexterdev/my-next-molecular-dy-1552651922</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 15 Mar 2019 12:15:06 GMT</pubDate></item><item><title><![CDATA[Tracking Interdigitated lipids from MD simulations]]></title><description><![CDATA[When using softwares like VMD to visualize membranes where lipids exhibit interdigitation as in our case, it will very useful if you can sort out those lipids which specifically exhibit this]]></description><link>https://ecency.com/@dexterdev/tracking-interdigita-1549802647</link><guid isPermaLink="true">https://ecency.com/@dexterdev/tracking-interdigita-1549802647</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 10 Feb 2019 12:47:03 GMT</pubDate><enclosure url="https://i.ecency.com/0x0/https://i.imgur.com/DbWoeI7.gif" length="0" type="image/gif"/></item><item><title><![CDATA[Visualizing Lipid Defects in model membrane simulations]]></title><description><![CDATA[Recently we did some all-atom classical molecular dynamics simulations involving DMPC model membrane, Nogo66 membrane active protein, TIP3P water model and NaCl ions. We used CHARMM36 forcefield and ran]]></description><link>https://ecency.com/@dexterdev/visualizing-lipid-de-1549468204</link><guid isPermaLink="true">https://ecency.com/@dexterdev/visualizing-lipid-de-1549468204</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 06 Feb 2019 15:53:00 GMT</pubDate><enclosure url="https://i.ecency.com/p/2gsjgna1uruvUuS7ndh9YqVwYGPLVszbFLwwpAYXZAmoq2YafDGmFjbBt6mDN5JhNGRpfcYPMjPyRBVPxaVSb5NfaeCZwRmRAC8srNtqV1EXxZf15p?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Mutated Nogo66 protein all atom classical molecular dynamics simulation video (50ns)]]></title><description><![CDATA[Below is a youtube video of 50 nanoseconds long trajectory of a recent all-atom molecular dynamics simulation which I did using NAMD software. The yellow dots are sodium ions and cyan dots are chloride]]></description><link>https://ecency.com/@dexterdev/mutated-nogo66-prote</link><guid isPermaLink="true">https://ecency.com/@dexterdev/mutated-nogo66-prote</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Thu, 24 Jan 2019 11:35:57 GMT</pubDate><enclosure url="https://i.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dwsrfYBSt5Ni5sfm7fHMXn9ypQUxs8npCdk?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A glimpse from my current work]]></title><description><![CDATA[Below is a video of two 400ns long all-atom classical molecular dynamics trajectories of Rap:Raf complex. The "ice blue" and "orange" tubes are Rap:Raf complex with phosphorylated Serine]]></description><link>https://ecency.com/@dexterdev/a-glimpse-from-my-cu</link><guid isPermaLink="true">https://ecency.com/@dexterdev/a-glimpse-from-my-cu</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 20 Jan 2019 15:43:27 GMT</pubDate><enclosure url="https://i.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dvHRjDe7Juj48LaZdFS3XpAb9NsNBS7ABaW?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Understanding Correlation measurements of Protein motions from MD trajectories]]></title><description><![CDATA[Today let us try understanding correlation maps. It is very common to see correlation maps of protein motions in molecular dynamics research papers. For example, see the figure below: A typical correlation]]></description><link>https://ecency.com/@dexterdev/understanding-correlation-measurements-of-protein-motions-from-md-trajectories</link><guid isPermaLink="true">https://ecency.com/@dexterdev/understanding-correlation-measurements-of-protein-motions-from-md-trajectories</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 24 Dec 2018 10:09:12 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn9R7fdFwCXX6RLT8?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Why SER11 site was chosen as the phosphorylation site? :  A frequent question which we encounter regarding our work]]></title><description><![CDATA[Hi friends... Recently I had written about our research work which got published in this August. Those who have not read that article can find it below: Phosphorylation promotes binding affinity of Rap-Raf]]></description><link>https://ecency.com/@dexterdev/why-ser11-site-was-chosen-as-the-phosphorylation-site-a-frequent-question-which-we-encounter-regarding-our-work</link><guid isPermaLink="true">https://ecency.com/@dexterdev/why-ser11-site-was-chosen-as-the-phosphorylation-site-a-frequent-question-which-we-encounter-regarding-our-work</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 14 Dec 2018 10:36:36 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnCw56vBDMsrW8tKY?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Phosphorylation promotes binding affinity of Rap-Raf complex [Original Research Work Summary]]]></title><description><![CDATA[Hello, my dear friends! Welcome to yet another science article from @dexterdev. Today I am going to write about something which I was thinking to do for the last few months. This is about my first research]]></description><link>https://ecency.com/@dexterdev/phosphorylation-promotes-binding-affinity-of-rap-raf-complex-original-research-work-summary</link><guid isPermaLink="true">https://ecency.com/@dexterdev/phosphorylation-promotes-binding-affinity-of-rap-raf-complex-original-research-work-summary</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 05 Dec 2018 16:27:06 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn4z35GgfhNhCASoY?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Addendum to my previous post: PCA caveat + Tracking Ubiquitin in the Principal component space]]></title><description><![CDATA[This is an addendum to my previous post which you can see here: Repository PCA caveat From PCA plots it is possible to create normalized histograms or distribution plots based on the density of scatter]]></description><link>https://ecency.com/@dexterdev/addendum-to-my-previous-post-pca-caveat-tracking-ubiquitin-in-the-principal-component-space</link><guid isPermaLink="true">https://ecency.com/@dexterdev/addendum-to-my-previous-post-pca-caveat-tracking-ubiquitin-in-the-principal-component-space</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sat, 01 Dec 2018 13:40:33 GMT</pubDate><enclosure url="https://i.ecency.com/p/C3TZR1g81UNaPs7vzNXHueW5ZM76DSHWEY7onmfLxcK2iNuXfzCmccV7N2nUPgp2ag7owMKYczUGrTUmwrPimPTgRGj5pwwnUaVbdtTCcyfwBrk4WKMdFxS?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Studying fluctuations in proteins from Molecular Dynamics trajectories]]></title><description><![CDATA[Hi friends... Welcome to yet another article from @dexterdev. Molecules are not stationary entities. Most of the molecules function via dancing in particular patterns. Their motions under different external]]></description><link>https://ecency.com/@dexterdev/studying-global-motions-of-proteins-from-molecular-dynamics-trajectories</link><guid isPermaLink="true">https://ecency.com/@dexterdev/studying-global-motions-of-proteins-from-molecular-dynamics-trajectories</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 28 Nov 2018 09:45:09 GMT</pubDate><enclosure url="https://i.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnK5Na25J7GqLAmJ5?format=match&amp;mode=fit" length="0" type="false"/></item></channel></rss>