<!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 20/10/2010 10:26 PM, shahab shariati wrote:
<blockquote
cite="mid:AANLkTinuqH3JU6=kRPpNPDe7oWHLL128asJrdt7fGzba@mail.gmail.com"
type="cite">
<p class="MsoNormal" style="margin: 0in 0in 0pt; line-height:
normal;"><span style="font-family: 'Times New Roman','serif';"><font
size="3">Dear Mark</font></span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt; line-height:
normal;"><span style="font-family: 'Times New Roman','serif';"><font
size="3"> </font></span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt; line-height:
normal;"><span style="font-family: 'Times New Roman','serif';"><font
size="3">you said in answer to -pbc nojump that using of new
xtc file for analysis section depends what one wants to
observe.</font></span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt; line-height:
normal;"><span style="font-family: 'Times New Roman','serif';"><font
size="3"> </font></span></p>
<p class="MsoNormal" style="margin: 0in 0in 6pt; line-height:
normal;"><span style="font-family: 'Times New Roman','serif';"><font
size="3">what observations is relevant to periodicity?</font></span></p>
</blockquote>
<br>
Anything that measures where something is relative to another.
Normally one is only interested in the nearest periodic image. IIRC,
some of the GROMACS tools are PBC-aware and determine the nearest
suitable for themselves, other times they treat the trajectory as if
there were no periodicity. In the latter case, if your results will
be sensitive to the actual locations of atoms with respect to the
periodic cell, then you'll wish to use trjconv to choose the
configuration best suited to your needs. In the analysis desired the
original post, the waters should all be in the same cell as the
DNA+protein interstice, hence centering the cell on that group, and
putting all waters into the cell.<br>
<br>
Mark<br>
</body>
</html>