<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 1/01/2012 9:38 PM, banafsheh mehrazma wrote:
<blockquote
cite="mid:1325414321.36893.YahooMailNeo@web160304.mail.bf1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div><span></span></div>
<div>Hi everyone, <br>
</div>
<div style="font-size: 12pt; font-family: 'times new roman','new
york',times,serif;">
<div style="font-size: 12pt; font-family: 'times new
roman','new york',times,serif;">
<div id="yiv1106543527">
<div>
<div style="color: rgb(0, 0, 0); background-color:
rgb(255, 255, 255); font-size: 12pt; font-family:
'times new roman','new york',times,serif;">
<div>I am studying a paper about a DNA simulation
using Gromacs and I encountered this in ion
addition step:</div>
<div>
<div>Na+ were added by replacing a solvent molecule
at ca. 6 Å</div>
<div>from the phosphorus in the direction of the
bisector of the angle</div>
<div>∠O1P-P-O2P (O1P and O2P being the phosphate
nonbridging</div>
<div>oxygen atoms)</div>
<div>I think what it means is that Na+ was added in
a distance of 6 Å from the phosphorus. How can we
specify this in GROMACS?</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
You'll need to find one manually. Set up some index groups and use
them with g_dist to measure distances. Or whatever else floats your
boat.<br>
<br>
Mark<br>
</body>
</html>