<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<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:0in;
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:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
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]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Dear gmx_users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have a question regarding the 4.5.4 version of gromacs, and the g_energy program.
<o:p></o:p></p>
<p class="MsoNormal">In the past I had used g_energy with the -aver option, which would give me partial
<o:p></o:p></p>
<p class="MsoNormal">sums along with my instantaneous energy values at each output step. This allowed
<o:p></o:p></p>
<p class="MsoNormal">me to take the difference between two successive partial sums divided by the my
<o:p></o:p></p>
<p class="MsoNormal">nstenergy value to get the average energy over that output period. Now when I use<o:p></o:p></p>
<p class="MsoNormal">the -aver option my output contains my instantaneous value, and what is said to be<o:p></o:p></p>
<p class="MsoNormal">the exact average. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have the feeling that this exact average is what I used to calculate by hand, i.e<o:p></o:p></p>
<p class="MsoNormal">the average of the energy over each output period. I tried to test this by calculating<o:p></o:p></p>
<p class="MsoNormal">the average by hand using gmxdump and my ener.edr file and my numbers match up<o:p></o:p></p>
<p class="MsoNormal"> to the fourth decimal place, but aren't exactly the same. Is this difference simply
<o:p></o:p></p>
<p class="MsoNormal">because gmxdump is truncating the energy values and giving them to me at lower
<o:p></o:p></p>
<p class="MsoNormal">precision? Am I correct on my assumption of what this –aver option is giving me?<o:p></o:p></p>
<p class="MsoNormal">Any guidance would be appreciated as I'm not so good at understanding the source<o:p></o:p></p>
<p class="MsoNormal">code.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you in advance<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Jake Spooner<o:p></o:p></p>
</div>
</body>
</html>