<div dir="ltr">Hi Tsjerk,<br><br>It means the resulting trajectory is free from translational and rotational degrees of freedom which I can use for the studies of internal dynamics i suppose.<br><br>Ram.<br><br><br><div class="gmail_quote">
On Wed, Sep 10, 2008 at 3:05 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Ram,<br>
<br>
-fit rot+trans performs an ordinary least-squares fit using the<br>
reference structure provided with -s, removing rotational and<br>
translational degrees of freedom.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="Wj3C7c"><br>
On Tue, Sep 9, 2008 at 9:47 PM, rams rams <<a href="mailto:rams.crux@gmail.com">rams.crux@gmail.com</a>> wrote:<br>
> Dear Users,<br>
><br>
> I have a question about the option -fit in trjconv.<br>
><br>
> The default option with -fit is none. If I use the option as rot+trans, does<br>
> it mean that the rotational and translational motions are removed from the<br>
> trajectory ? If not, is there any option in gromacs, to create a<br>
> translational and rotational free trajectory from the original trajecotry<br>
> file ? I also want to make sure the usage of the command:<br>
><br>
> trjconv -f original trr -s .tpr -o rot_trans_free.trr -fit rot+trans<br>
><br>
> Thanks in advance.<br>
><br>
> Ram.<br>
><br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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