Hai Sir ! <br> Actually i want to see the dihedral angle (Câ-S-S-Câ) variation over time.I used the commands<br> <br>"g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all"<br>
<br>"g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all"<br> <br>Please suggest me the right options<br>Thanks for ur concern<br> <br><br><div class="gmail_quote">2009/4/1 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">Hi Venkat,<br>
<br>
What exactly do you mean with variations. Do you want to follow the<br>
angle over time, or do you want distributions with mean and variance<br>
estimates? g_angle and g_chi seem to be the appropriate tools. You<br>
mention you tried all suitable options, but fail to explain what you<br>
tried and what exactly it is you want. We need that sort of<br>
information to be able to help you out.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
2009/4/1 Venkat Reddy <<a href="mailto:venkat4bt@gmail.com">venkat4bt@gmail.com</a>>:<br>
<div><div></div><div class="h5">> First of all Thanks for ur reply !<br>
> I tried both g_angle and g_chi with all suitable options, but i didn't get<br>
> the required result.Can u plz help me in this regard ???<br>
><br>
> 2009/4/1 Antonia V. <<a href="mailto:antonia_haha@hotmail.com">antonia_haha@hotmail.com</a>><br>
>><br>
>> Did you try g_angle??<br>
>><br>
>> Antonia<br>
>> ________________________________<br>
>> Date: Wed, 1 Apr 2009 11:35:29 +0530<br>
>> From: <a href="mailto:venkat4bt@gmail.com">venkat4bt@gmail.com</a><br>
>> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> Subject: [gmx-users] How to calculate the dihedral angle variations ???<br>
>><br>
>> Hi Everyone !<br>
>> How can i see the variations in the "Câ-S-S-Câ" (Disulfide bridge)<br>
>> dihedral angle during a simulation ?????<br>
>> Thanks in advance<br>
>><br>
>><br>
>><br>
>> Cheers from<br>
>> Venkat Reddy Chirasani<br>
>> M.Tech Bioinformatics<br>
>> UNIVERSITY OF HYDERABAD<br>
>><br>
>> ________________________________<br>
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><br>
><br>
><br>
> --<br>
> Venkat Reddy Chirasani<br>
> M.Tech Bioinformatics<br>
> UNIVERSITY OF HYDERABAD<br>
><br>
> _______________________________________________<br>
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><br>
<br>
<br>
<br>
--<br>
</div></div>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>
<div><div></div><div class="h5">_______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Venkat Reddy Chirasani<br>M.Tech Bioinformatics<br>UNIVERSITY OF HYDERABAD<br>