I'm sorry, actually I forgot to add the flag in the email but I added it when I started the program.<br><br>g_angle -f traj.trr -s topol.tpr -n dihe.ndx -oh histo.xvg -type dihedral<br>I get the following output:<br><br>
Group 0 (Phi=0.0_3_5.92) has 232 elements<br>There is one group in the index<br>Reading file diheA3.tpr, VERSION 3.3.3 (single precision)<br>trn version: GMX_trn_file (single precision)<br>Last frame 10000 time 20000.000 <br>
Found points in the range from 0 to 359 (max 360)<br> < angle > = 0.374572<br>< angle^2 > = 262.338<br>Std. Dev. = 16.1925<br>Order parameter S^2 = 0.344698<br><br>but it generates only a angdist.xvg file.<br>
I'm wondering why it's not generating the histo.xvg file.<br>Thanks for your help!<br><br><div class="gmail_quote">2011/10/4 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Giulio Tesei 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!<br>
I'm performing the analysis of a 30 residues PVA polymer chain in SPC water.<br>
I'm trying to find the dihedral transition times of each residue (possibly as an histogram 'number of transitions vs. residue number').<br>
I've already tried:<br>
<br>
1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh histo.xvg<br>
but it gives no output besides angdist.xvg<br>
<br>
</blockquote>
<br></div>
Add "-type dihedral" to this command, otherwise the analysis is for normal angles.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2) g_dih -f traj.trr -s topol.tpr -o dihe.out<br>
but it gives no output besides an empty dihe.out<br>
<br>
3) g_chi (it says there are no dihedral angles in the structure. I guess that this program is for proteins only and it doesn't recognize PVA backbone dihedrals...).<br>
I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.<br>
<br>
Thanks for any incoming help!<br>
<br>
Giulio<br>
<br>
</blockquote>
<br></div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <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/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the 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/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br>