Hi Mark,<div><br></div><div>Ok here is the command line i used :-</div><div><br></div><div>g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all </div><div><br></div><div>output is </div><div><br></div><div>
<div># This file was created Tue Dec 1 20:20:41 2009</div><div># by the following command:</div><div># g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all</div><div>#</div><div># g_angle is part of G R O M A C S:</div>
<div>#</div><div># Go Rough, Oppose Many Angry Chinese Serial killers</div><div>#</div><div>@ title "Dihedral Distribution: C34_C36_C37_C38"</div><div>@ xaxis label "Degrees"</div><div>@ yaxis label ""</div>
<div>@TYPE xy</div><div>@ subtitle "average angle: 9.87432\So\N"</div><div>@with g0</div><div>@ world xmin -180</div><div>@ world xmax 180</div><div>@ world ymin 0</div><div>@ world ymax 0.0451172</div>
<div>@ xaxis tick major 60</div><div>@ xaxis tick minor 30</div><div>@ yaxis tick major 0.005</div><div>@ yaxis tick minor 0.0025</div><div> -180 0.015625</div><div> -179 0.011719</div><div>
-178 0.015625</div><div> -177 0.000000</div><div> -176 0.035156</div><div> -175 0.031250</div><div> -174 0.019531</div><div> -173 0.019531</div><div> -172 0.023438</div>
<div> -171 0.015625</div><div> -170 0.015625</div><div><br></div><div>I did not include the distribution for rest of the angles.</div><div> </div><div>The second column is the fractional distribution of dihedrals with the corresponding angle in the 1st column.</div>
<div><br></div><div>The distribution is averaged over time t = 800ps and 802 ps snapshots. I checked this part.</div><div><br></div><div>Amit</div></div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">
On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Mark,<br>
<br>
It does seem that the -all option averages the distributions. The thing is i was confused with "the first graph is the average, the rest are the individual angles." because when i tried it previously i only found 2 columns which were angle and distribution.<br>
<br>
But now i checked again explicitly by doing few more g_angle commands and it seems that -all does do what i wanted to do. I still dont know what the "rest are the individual angles" means. <br>
</blockquote>
<br></div>
I haven't ever used it, but would have expected the output to be along the lines of<br>
<br>
Time "Average over all angles" Angle-1 Angle-2 ...<br>
1 234 23 345<br>
2 123 234 232<br>
2 223 ...<br>
3 323<br>
<br>
What output do you get and what seems wrong to you?<br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
Amit Choubey wrote:<br>
<br>
Hi everyone,<br>
<br>
I am trying to analyze dihedrals of molecules after a<br>
simulation. I am able to calculate dihedral distribution at ant<br>
particular time using g<br>
-angle and proper group using<br>
<br>
g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od<br>
dihed12<br>
<br>
This gives me the distribution at t=800 ps . What i really want<br>
is to see the dihedral distribution at all time steps (after 800<br>
ps) in one go, and may be do some averaging later. Is there a<br>
straight forward way to do this. I can imagine that i could<br>
write a script file that could do this but then i dont want to<br>
deal with a lot of files, i rather want everything to be saved<br>
in a single file with multiple columns. Could someone suggest a<br>
trick for this?<br>
<br>
<br>
The first paragraph of g_angle -h suggests there's an option where<br>
"the first graph is the average, the rest are the individual<br>
angles." Does this work?<br>
<br>
<br>
Mark<br>
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