Thank you for your replies,<br>indeed it worked!<br>But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures.<br><br>Carla <br>
<br><div class="gmail_quote">On Thu, Feb 25, 2010 at 11:55 AM, Amir Marcovitz <span dir="ltr"><<a href="mailto:amarcovitz@gmail.com">amarcovitz@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;">
<div dir="ltr"><div>Hi,</div>
<div> </div>
<div>if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx)</div>
<div> </div>
<div>the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution</div>
<div> </div>
<div>cheers<br><br></div>
<div class="gmail_quote"><div><div></div><div class="h5">On Wed, Feb 24, 2010 at 10:22 PM, Carla Jamous <span dir="ltr"><<a href="mailto:carlajamous@gmail.com" target="_blank">carlajamous@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">Hi everyone,<br>please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average.<br>
<br>Thanks,<br><font color="#888888">Carla<br></font><br></div></div>--<div class="im"><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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