<br><br><div class="gmail_quote">On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
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><div class="im">
That is true. But what does the manual refer to when it says <br>
the first graph is the average, the rest are the individual angles<br>
<br>
what and where are the rest? I am only curious because there might be a hidden feature that could be useful for me.<br>
<br>
</div></blockquote>
<br>
Read all of the help information; the command in the .xvg file below shows that you're not yet using the right output options. Hint: look at the sentence in g_angle -h before the one quoted above, as well as the -ov flag...<br>
</blockquote><div><br></div><div>-ov flag gives the average value of angle of the group with time. This is not very useful for me right now.</div><div><br></div><div>I am interested in the distribution of dihedrals with angle. </div>
<div><br></div><div>I was just curious about the -all features...</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Amit<div><div></div><div class="h5"><br>
<br>
On Wed, Dec 2, 2009 at 12:21 AM, 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 Mark,<br>
<br>
Ok here is the command line i used :-<br>
<br>
g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e<br>
804 -all<br>
output is<br>
# This file was created Tue Dec 1 20:20:41 2009<br>
# by the following command:<br>
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e<br>
804 -all<br>
#<br>
# g_angle is part of G R O M A C S:<br>
#<br>
# Go Rough, Oppose Many Angry Chinese Serial killers<br>
#<br>
@ title "Dihedral Distribution: C34_C36_C37_C38"<br>
<br>
<br>
This title makes it look like there is only one angle in your index<br>
file.<br>
<br>
Mark<br>
<br>
@ xaxis label "Degrees"<br>
@ yaxis label ""<br>
@TYPE xy<br>
@ subtitle "average angle: 9.87432\So\N"<br>
@with g0<br>
@ world xmin -180<br>
@ world xmax 180<br>
@ world ymin 0<br>
@ world ymax 0.0451172<br>
@ xaxis tick major 60<br>
@ xaxis tick minor 30<br>
@ yaxis tick major 0.005<br>
@ yaxis tick minor 0.0025<br>
-180 0.015625<br>
-179 0.011719<br>
-178 0.015625<br>
-177 0.000000<br>
-176 0.035156<br>
-175 0.031250<br>
-174 0.019531<br>
-173 0.019531<br>
-172 0.023438<br>
-171 0.015625<br>
-170 0.015625<br>
<br>
I did not include the distribution for rest of the angles.<br>
The second column is the fractional distribution of dihedrals<br>
with the corresponding angle in the 1st column.<br>
<br>
The distribution is averaged over time t = 800ps and 802 ps<br>
snapshots. I checked this part.<br>
<br>
Amit<br>
<br>
<br>
<br>
<br>
On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham<br>
<<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>><br></div></div><div><div>
</div><div class="h5">
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<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 Mark,<br>
<br>
It does seem that the -all option averages the distributions.<br>
The thing is i was confused with "the first graph is the<br>
average, the rest are the individual angles." because when i<br>
tried it previously i only found 2 columns which were<br>
angle and<br>
distribution.<br>
<br>
But now i checked again explicitly by doing few more g_angle<br>
commands and it seems that -all does do what i wanted to<br>
do. I<br>
still dont know what the "rest are the individual angles"<br>
means.<br>
<br>
<br>
I haven't ever used it, but would have expected the output to be<br>
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>
On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham<br>
<<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>><br>
<mailto:<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>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<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<br>
distribution<br>
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<br>
chain1.ndx -od<br>
dihed12<br>
<br>
This gives me the distribution at t=800 ps . What i<br>
really want<br>
is to see the dihedral distribution at all time steps<br>
(after 800<br>
ps) in one go, and may be do some averaging later.<br>
Is there a<br>
straight forward way to do this. I can imagine<br>
that i could<br>
write a script file that could do this but then i dont<br>
want to<br>
deal with a lot of files, i rather want everything<br>
to be<br>
saved<br>
in a single file with multiple columns. Could someone<br>
suggest a<br>
trick for this?<br>
<br>
<br>
The first paragraph of g_angle -h suggests there's an<br>
option<br>
where<br>
"the first graph is the average, the rest are the<br>
individual<br>
angles." Does this work?<br>
<br>
<br>
Mark<br>
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</div></div></blockquote>
<br>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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