Hi Mark,<div><br></div><div>It does seem that the -all option averages the distributions. The thing is i was confused with <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">"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.</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><span class="Apple-style-span" style="font-size: 13px; "></span><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">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. </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Thank you,</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Amit<br></span></font><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div>
<div><br></div><div><div class="gmail_quote">On Tue, Dec 1, 2009 at 6:52 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><div></div><div class="h5">Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everyone,<br>
<br>
I am trying to analyze dihedrals of molecules after a simulation. I am able to calculate dihedral distribution at ant 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 dihed12<br>
<br>
This gives me the distribution at t=800 ps . What i really want is to see the dihedral distribution at all time steps (after 800 ps) in one go, and may be do some averaging later. Is there a straight forward way to do this. I can imagine that i could write a script file that could do this but then i dont want to deal with a lot of files, i rather want everything to be saved in a single file with multiple columns. Could someone suggest a trick for this?<br>
</blockquote>
<br></div></div>
The first paragraph of g_angle -h suggests there's an option where "the first graph is the average, the rest are the individual angles." Does this work?<div><div></div><div class="h5"><br>
<br>
Mark<br>
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