<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Dear Markus,<br>
If you know the residues composing the cavity (and I think you know
it), you can simply change the coordinates <br>
of the water molecule in the .gro file to move the water in the
cavity.<br>
<br>
Francesco<br>
<br>
<br>
Il 12/10/2011 18:17, Markus Weingarth ha scritto:
<blockquote
cite="mid:890698725.50900.1318436277033.JavaMail.fmail@mwmweb008"
type="cite"><br>
Dear Gromacs-users,<br>
<br>
I would like to force an arbitrary water molcule from the box into
an occluded cavity of a membrane-channel. It do not want this
water molcule within the cavity at the beginning of the
simulation.<br>
<br>
I though that I could implement intermolecular distance restraints
between a water residue an the protein, but I did not manage that
and all the suggestions I found here to implement intermolecular
distance restraints seem not to work out for water - protein
contacts. Does anybody has a suggestion how to implement such
restraints ? Would the pull-code an option for my problem ?<br>
<br>
Thank you very much<br>
Markus<br>
<br>
<br>
<br>
<br>
<br>
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td bgcolor="#000000"><img moz-do-not-send="true"
src="https://img.ui-portal.de/p.gif" alt="" height="1"
border="0" width="1"></td>
</tr>
<tr>
<td style="font-family:verdana; font-size:12px;
line-height:17px;">SMS schreiben mit WEB.DE FreeMail -
einfach, schnell und <br>
kostenguenstig. Jetzt gleich testen! <a
moz-do-not-send="true" href="http://f.web.de/?mc=021192"><b>http://f.web.de/?mc=021192</b></a></td>
</tr>
</tbody>
</table>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>