Yes -ov does give you average angle as a function of time. I am not sure if this answers your question though.<br><br><div>amit</div><div><br><div class="gmail_quote">On Fri, Jan 7, 2011 at 2:40 AM, Carla Jamous <span dir="ltr"><<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Thank you, <br><br>It worked, one last question. Something is not very clear to me:<br><br>-ov: plots the average angle of a group of angles as a function of time!! What does it mean? <br>
<br>Because I'm getting positive and negative values in the same plot. Are these values the values of my dihedral angle as a function of time?<br>
<br>Thanks again,<br><font color="#888888">Carla</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
try the -type option with dihedral<div><br></div><div><font color="#888888">amit<br><br></font><div class="gmail_quote"><div><div></div><div>On Fri, Jan 7, 2011 at 2:16 AM, 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="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><div><div></div><div>Hi Everyone,<br><br>Please I'm trying to calculate one dihedral angle as a function of time during my simulation.<br>
For this, I used g_angle. In the manual (version 4.0.3) it says: the indexfile should contain atom-triplets or atom-quadruplets for dihedrals.<br>
<br>I put an atom-quadruplet in my index file, but when I run <br>g_angle -f .xtc -n .ndx -od .xvg <br><br>and I select the group of atom-quadruplets, gromacs crashes and shows this error message:<br>number of index elements not multiple of 3, these can not be angle triplets<br>
<br>So actually g_angle only calculates angles not dihedrals?<br><br>Thanks<br><font color="#888888"><br>Carla<br><br>
</font><br></div></div>--<div><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>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></blockquote></div><br></div>
<br>--<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>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br></div>