<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 15/12/2010 1:03 PM, Tom Dupree wrote:
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal">Greetings all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We are looking at setting up Linux desktop
in our lab for setting up some simulations to be run
externally, as well some short simulations.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am new to Linux and Gromos.</p>
</div>
</blockquote>
<br>
I'm going to presume you mean GROMACS.<br>
<br>
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have done some reading of the gmx-users
list archive and have a few questions.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I was wondering if there is anything in
particular to avoid/choose in terms of hardware for such a
system?</p>
</div>
</blockquote>
<br>
Since you are not running with MPI parallelism, no.<br>
<br>
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal">Specifically does Gromos prefer a
particular architecture? (INTEL/AMD)</p>
</div>
</blockquote>
<br>
No. Any chip with SSE or SSE2 is fine.<br>
<br>
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal">I understand there is now some GPU
computing support with Gromos, are there any problems using
consumer grade cards? (GeForce GTX 460/480)</p>
</div>
</blockquote>
<br>
The manual lists some compatible cards.<br>
<br>
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal">Is Gromos happier in a particular flavour
of Linux, given we will be running on a desktop? </p>
</div>
</blockquote>
<br>
No. Some distros do have GROMACS available via their package
managers (usually in their "extras" section).<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1FFC0F40B2B7CF44A5FBC162C2469DD035926A89B0@INFPWEC003.ad.unsw.edu.au"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your time in looking at these
(noobish) questions.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Tom<o:p></o:p></p>
</div>
</blockquote>
<br>
</body>
</html>