<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">On 17/09/2012 4:21 PM, Anik Sen wrote:<br>
</div>
<blockquote
cite="mid:BDE9D87D31C781498280133FD1BE69A54B26E046@EXCHANGE.csmcri.org"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<style type="text/css" id="owaParaStyle"></style>
<div style="direction:ltr; font-family:Tahoma; color:#000000;
font-size:10pt">Hello,
<div> This is Anik Sen from India. Am using Gromacs
4.5.5. to do some calculations on solvation and ligand binding
interactions with DNA. I have some questions regarding the
problem. </div>
<div><br>
</div>
<div>As water is present in the system, so according to the
manual the define in the .mdp file must be -DFLEXIBLE. No
probem in that.</div>
<div>But I read in different works by other people that for DNA
they are using NPT ensemble. But there are two couplings in
the .mdp file. </div>
<div>1. temparature coupling </div>
<div>2. Pressure coupling</div>
<div><br>
</div>
<div>I want to ask that which coupling will be better for
temperature; </div>
<div>a. Berendsen coupling</div>
<div>b. V-rescale coupling</div>
<div>c. nose-hoover coupling</div>
<div><br>
</div>
<div>AND for pressure:</div>
<div>a. Berendsen coupling</div>
<div>b. Parrinello-Rahman coupling</div>
<div>c. Martyna-Tuckerman-Tobias-Klein implementation coupling</div>
<div><br>
</div>
<div>I am also little confused over the pcoupltype, where
options are isotropic; semi-isotropic and anisotropic.</div>
<div>Please help me in this matter.</div>
<div>Thanks in advance;</div>
</div>
</blockquote>
<br>
These are not questions about development of GROMACS. Please ask in
the correct forum.<br>
<br>
Mark<br>
</body>
</html>