<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>Re: [gmx-users] g_dipoles, average not the same as from g_analyze</title>
<META http-equiv=Content-Type content="text/html; charset=windows-1251">
<meta http-equiv="Content-Style-Type" content="text/css">
<style type="text/css"><!--
body {
margin: 5px 5px 5px 5px;
background-color: #ffffff;
}
/* ========== Text Styles ========== */
hr { color: #000000}
body, table /* Normal text */
{
font-size: 9pt;
font-family: 'Courier New';
font-style: normal;
font-weight: normal;
color: #000000;
text-decoration: none;
}
span.rvts1 /* Heading */
{
font-size: 10pt;
font-family: 'Arial';
font-weight: bold;
color: #0000ff;
}
span.rvts2 /* Subheading */
{
font-size: 10pt;
font-family: 'Arial';
font-weight: bold;
color: #000080;
}
span.rvts3 /* Keywords */
{
font-size: 10pt;
font-family: 'Arial';
font-style: italic;
color: #800000;
}
a.rvts4, span.rvts4 /* Jump 1 */
{
font-size: 10pt;
font-family: 'Arial';
color: #008000;
text-decoration: underline;
}
a.rvts5, span.rvts5 /* Jump 2 */
{
font-size: 10pt;
font-family: 'Arial';
color: #008000;
text-decoration: underline;
}
span.rvts6
{
font-weight: bold;
color: #800000;
}
span.rvts7
{
font-size: 8pt;
font-family: 'arial';
font-style: italic;
color: #c0c0c0;
}
a.rvts8, span.rvts8
{
font-size: 8pt;
font-family: 'arial';
color: #0000ff;
text-decoration: underline;
}
a.rvts9, span.rvts9
{
color: #0000ff;
text-decoration: underline;
}
/* ========== Para Styles ========== */
p,ul,ol /* Paragraph Style */
{
text-align: left;
text-indent: 0px;
padding: 0px 0px 0px 0px;
margin: 0px 0px 0px 0px;
}
.rvps1 /* Centered */
{
text-align: center;
}
--></style>
</head>
<body>
<p>Dear Emanuel,</p>
<p><br></p>
<p>Please, check </p>
<p><a class=rvts9 href="http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html">http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html</a></p>
<p>and Berk reply.</p>
<p><br></p>
<p>I did never use -av (-a ?) option, maybe there is similar bug in average.xvg. </p>
<p>Anyway last column of Mtot.xvg gives really correct norm of M_tot vector!</p>
<p><span class=rvts7><br></span></p>
<p><span class=rvts7>Regards,</span></p>
<p><span class=rvts7> Dmitri </span></p>
<p><br></p>
<p>---------</p>
<p><span class=rvts6>> Dear gromacs users,</span></p>
<p><br></p>
<p><span class=rvts6>> Sorry but my last email was not correct. </span></p>
<p><span class=rvts6>> I have following question:</span></p>
<p><br></p>
<p><span class=rvts6>> With the use of the g_dipoles tool I have analysed the average</span></p>
<p><span class=rvts6>> dipole moment using following command:</span></p>
<p><br></p>
<p><span class=rvts6>> g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg </span></p>
<p><br></p>
<p><span class=rvts6>> I think the option -av calculates the average of the dipole moment of the system I have chosen.</span></p>
<p><br></p>
<p><span class=rvts6>> Following output is given:</span></p>
<p><br></p>
<p><span class=rvts6>> x1 = time (ps)</span></p>
<p><span class=rvts6>> y1 = aver1</span></p>
<p><span class=rvts6>> y2 = aver2**2</span></p>
<p><span class=rvts6>> y3 = aver1 - aver2**2</span></p>
<p><span class=rvts6>> ...</span></p>
<p><br></p>
<p><span class=rvts6>> I have taken the root of aver2 (y2^(1/2)) to get and plotted that against x1.</span></p>
<p><br></p>
<p><span class=rvts6>> Mtot.xvg corresponds to the following quantities:</span></p>
<p><br></p>
<p><span class=rvts6>> x1 = time (ps)</span></p>
<p><br></p>
<p><span class=rvts6>> y1 = M_x</span></p>
<p><span class=rvts6>> y2 = M_y</span></p>
<p><span class=rvts6>> y3 = M_z</span></p>
<p><span class=rvts6>> y4 = M_tot</span></p>
<p><br></p>
<p><span class=rvts6>> I plotted M_tot against time and calculated the average by using g_analyze.</span></p>
<p><span class=rvts6>> Now I have following problem:</span></p>
<p><span class=rvts6>> My average value from g_analyze is not equal to the value of which I received from g_dipoles.</span></p>
<p><span class=rvts6>> The difference between the two values is at about 20 Debye. </span></p>
<p><span class=rvts6>> Could you tell me the reason why there exists a difference?</span></p>
<p><span class=rvts6>> Does g_dipoles calculate the average in another way than g_analyze?</span></p>
<p><br></p>
<p><span class=rvts6>> Thank you for your kind answer in advance.</span></p>
<p><br></p>
<p><span class=rvts6>> Best regards,</span></p>
<p><br></p>
<p><span class=rvts6>> Emanuel Peter</span></p>
</body></html>