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softwares.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>PKMLab | Softwares</title>
<!-- Favicon -->
<link rel="shortcut icon" href="images/favicon.ico" type="image/x-icon">
<!-- Font awesome -->
<link href="as/3/font-awesome.css" rel="stylesheet">
<!-- Bootstrap -->
<link href="as/3/bootstrap.css" rel="stylesheet">
<!-- Slick slider -->
<link rel="stylesheet" type="text/css" href="as/3/slick.css">
<!-- Date Picker -->
<link rel="stylesheet" type="text/css" href="as/3/bootstrap-datepicker.css">
<!-- Fancybox slider -->
<link rel="stylesheet" href="as/3/jquery.fancybox.css" type="text/css" media="screen" />
<!-- Theme color -->
<link id="switcher" href="as/3/theme-color/default-theme.css" rel="stylesheet">
<!-- Main style sheet -->
<link href="style.css" rel="stylesheet">
<!-- Google Fonts -->
<link href='https://fonts.googleapis.com/css?family=Tangerine' rel='stylesheet' type='text/css'>
<link href='https://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>
<link href='https://fonts.googleapis.com/css?family=Prata' rel='stylesheet' type='text/css'>
<!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<!--START SCROLL TOP BUTTON -->
<a class="scrollToTop" href="#">
<i class="fa fa-angle-up"></i>
<span>Top</span>
</a>
<!-- END SCROLL TOP BUTTON -->
<!-- Start header section -->
<header id="mu-header">
<nav class="navbar navbar-default mu-main-navbar" role="navigation">
<div class="container">
<div class="navbar-header">
<!-- FOR MOBILE VIEW COLLAPSED BUTTON -->
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
<span class="sr-only">Toggle navigation</span>
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</button>
<!-- LOGO -->
<a class="navbar-brand" href="index.html"><img src="images/logo_iisc.svg" alt="Logo img"></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul id="top-menu" class="nav navbar-nav navbar-right mu-main-nav">
<li><a href="index.html">HOME</a></li>
<li><a href="research.html">RESEARCH</a></li>
<li><a href="teaching.html">TEACHING</a></li>
<li><a href="publication.html">PUBLICATIONS</a></li>
<li><a href="softwares.html">SOFTWARES</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="group.html">GROUP <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="group-present.html">PRESENT</a></li>
<li><a href="group-past.html">ALUMNI</a></li>
</ul>
</li>
<li><a href="index.html#mu-contact">CONTACT</a></li>
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<a class="dropdown-toggle" data-toggle="dropdown" href="blog.html">OTHERS<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="gallery.html">GALLERY</a></li>
<li><a href="research-interest.html">RESEARCH INTEREST</a></li>
<li><a href="personal-interest.html">PERSONAL INTEREST</a></li>
</ul>
</li>
</ul>
</div><!--/.nav-collapse -->
</div>
</nav>
</header>
<!-- End header section -->
<!-- Start Group banner -->
<section id="mu-blog-banner">
<div class="container">
<div class="mu-blog-banner-area">
<h2>Softwares</h2>
</div>
</div>
</section>
<!-- End Blog banner -->
<!-- Start Softwares section -->
<section id="mu-software">
<div class="container">
<div class="mu-title">
</div>
<div class="row software-card fadeIn">
<div class="col-md-4">
<div class="card-image">
<img src="images/softwares_thumbnails/software_dendrimer_toolkit.jpg">
</div>
</div>
<div class="col-md-8 software-info">
<div class="row">
<div class="card-content">
<span class="card-title"><h2>Dendrimer Builder Toolkit (DBT)</h2></span>
<p>DBT can be used to build polymer (linear or hyperbranched) in AMBER depending upon multiplicity of joining residues (For more details please see tutorial and refer article: J. Comput. Chem. 2012, 33, 1997-2011).
Thus DBT is a graphical user interface (GUI) written in PERL-Tk, which generates a set of commands (xleap/tleap) to be used further by AMBER.
DBT has been integrated with AMBER10.
DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity and generation of dendrimer.
</p>
<p><b>Please refer: </b>
<u>
<li>Dendrimer Building Toolkit: Model Building and Characterization of Various Dendrimer Architectures
J. Comput. Chem., 2012, 33, 1997-2011</li>
</u>
</p>
<p><b>System requirements: </b>Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)</p>
</div>
</div>
<div class="row">
<div class="card-action">
<a href="http://www.physics.iisc.ernet.in/~maiti/dbt/home.html"><strong>DBT Website</strong></a>
<br>
</br>
<p><b>Equilibrium configurations of G3-G6 PAMAM dendrimers: </b> <a href="as/4/Dendrimer_Structure-pamam-EDA-allpH.zip"><strong> Here</strong></a></p>
</div>
</div>
</div>
</div>
<div class="row software-card fadeIn">
<div class="col-md-4">
<div class="card-image">
<img src="images/softwares_thumbnails/software_2PT.png" >
</div>
</div>
<div class="col-md-8 software-info">
<div class="row">
<div class="card-content">
<span class="card-title"><h2>Two-phase thermodynamic (2PT) model</h2></span>
<p>Two-phase thermodynamic (2PT) model is used for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations.
In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions.
A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component.
</p>
<p><b>Please refer: </b>
<u>
<li> Lin, S.T., Blanco, M. and Goddard III, W.A., 2003. The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids. The Journal of chemical physics, 119(22), pp.11792-11805.</li>
<li> Lin, S.T., Maiti, P.K. and Goddard III, W.A., 2010. Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. The Journal of Physical Chemistry B, 114(24), pp.8191-8198.</li>
</u>
</p>
<p><b>System requirements: </b>Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)</p>
</div>
</div>
<div class="row">
<div class="card-action">
Please contact us to avail this software.
</div>
</div>
</div>
</div>
</div>
</section>
<!-- Start Footer -->
<footer id="mu-footer">
<div class="container">
<div class="row">
<div class="col-md-12">
<div class="mu-footer-area">
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</footer>
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<!-- jQuery library -->
<script src="as/1/jquery.min.js"></script>
<!-- Bootstrap -->
<script src="as/1/bootstrap.js"></script>
<!-- Slick slider -->
<script type="text/javascript" src="as/1/slick.js"></script>
<!-- Counter -->
<script type="text/javascript" src="as/1/waypoints.js"></script>
<script type="text/javascript" src="as/1/jquery.counterup.js"></script>
<!-- Date Picker -->
<script type="text/javascript" src="as/1/bootstrap-datepicker.js"></script>
<!-- Mixit slider -->
<script type="text/javascript" src="as/1/jquery.mixitup.js"></script>
<!-- Add fancyBox -->
<script type="text/javascript" src="as/1/jquery.fancybox.pack.js"></script>
<!-- Custom js -->
<script src="as/1/custom.js"></script>
</body>
</html>