<p>Hey :)</p>
<p>Option -center shifts the system, which will show up as a component in the displacement.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On May 6, 2011 5:39 PM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><br><p><font color="#500050">
Tomek Wlodarski wrote:
>
> Dear Justin,
>
> Thanks, sure I will give more details.
>
> This comman...</font></p>
Are all the measurements being done in VMD, or are you using g_dist for any of these? If you're using g_dist, then some of the distances may be affected by using your old .tpr file, wherein the protein is perhaps not centered.<br>
<br>
If all of the measurements are being done in VMD, then I can't comment, but perhaps someone else can. It might be useful to show how you're doing these measurements. If you're not using g_dist, it would be interesting to see how the results of g_dist and VMD compare, in order to tease out the source of the difference.<br>
<font color="#888888">
<br>
-Justin</font><p><font color="#500050">
> Best!
>
> tomek
>
> On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:
>>...</font></p></blockquote></p>