<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>how to correct velocities in trajectory file</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-size: 8pt;
font-family: 'arial';
font-style: italic;
color: #c0c0c0;
}
a.rvts7, span.rvts7
{
font-size: 8pt;
font-family: 'arial';
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 gmx'ers,</p>
<p><br></p>
<p>I've done a long NVE simulation in vacuo. During this run I had to take care to diminish the total energy drift, so my choice was</p>
<p><br></p>
<p>comm_mode = None</p>
<p><br></p>
<p>Now, analysing a smaller subsystem (solute + shell of solvent) I want to exclude its COM movement. Sorry, I fail to find any instruction how to do it. Extracting the subset with</p>
<p><br></p>
<p>trjconv -f traj.trr -s -n my_index.ndx -o subset.trr -center </p>
<p><br></p>
<p>centers the subsystem well. But as it can be checked with</p>
<p><br></p>
<p>g_traj -f subset.trr -s subset.tpb -n my_index.ndx -ov -ekt -ekr -com</p>
<p><br></p>
<p>the velocities in subset.trr remain unchanged.</p>
<p>Ideally I would like, first, to correct the atom velocities to zero COM velocity, and next to correct them to obtain zero angular momentum of my subsystem. Could anyone advise me how to correct properly the velocities in trr-file?</p>
<p><br></p>
<p>Thank you in advance,</p>
<p><br></p>
<p><span class=rvts6>-- </span></p>
<p><span class=rvts6>Regards,</span></p>
<p><span class=rvts6> Dmitri </span><a class=rvts7 href="mailto:ddubov@ngs.ru">mailto:ddubov@ngs.ru</a></p>
</body></html>