<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 27/03/2012 8:23 AM, Roy Roshko wrote:
<blockquote
cite="mid:1E78CFC70CDD5E4A96A2A76B5E3B2EBFD45D6D@UMCE3EXMD01.ad.umanitoba.ca"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0,
0); font-size: 10pt;">
<p class="MsoNormal">Dear gromacs users,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Aside from a scale factor, should the time
dependence of the temperature T(t) extracted from the .trr
file with g_traj for a given residue be </p>
</div>
</blockquote>
<br>
Using what command line? Have you read g_traj -h about -ot?<br>
<br>
<blockquote
cite="mid:1E78CFC70CDD5E4A96A2A76B5E3B2EBFD45D6D@UMCE3EXMD01.ad.umanitoba.ca"
type="cite">
<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">
<p class="MsoNormal">identical to the time dependence of the
total kinetic energy (translational + rotational) K(t)
extracted from the .trr file with g_traj for the same residue?
If not, why not? Based on the formal relationship between the
kinetic energy and temperature (T ~ v^2) we expect them to be
identical but our simulations do not yield this result. Any
information would be much appreciated.</p>
<p class="MsoNormal"> <br>
</p>
</div>
</blockquote>
<br>
There are many things that affect the fine details here, including
GROMACS version, your integrator, thermostat and the frequency of
energy computation and output vs velocity output. So with the
available information there's nothing to say. Do check out chapter 3
of the manual for discussion of details here.<br>
<br>
Mark<br>
</body>
</html>