<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Dear all,<br>
how can i calculate the root-mean-square fluctuation (R<span>MSF)</span>(<span style="font-weight: bold;">last 5ns</span>) of a group of atoms <span style="font-weight: bold;">relative to their equilibrium position</span>?<br>
the command i have used is <br>
g_rmsf -f mer.xtc -s md_1ns.tpr -n group.ndx -o rmsf.xvg -nice 4 -b 35000 -e 36000 <span style="font-weight: bold;"><br>
</span>where, md_1ns.tpr is the starting tpr for the production run.<br>
Is this one correct? if not please suggest me the command for rmsf calculation after fitting <span style="font-weight: bold;">to a referencee frame</span>?<br>
Again the output file is like.........(with 10 atoms in a group)<br>
----------------------------------------------------------------------------<br>
# GRowing Old MAkes el Chrono Sweat<br>
#<br>
@ title "RMS fluctuation"<br>
@ xaxis label "Atom"<br>
@ yaxis label "(nm)"<br>
@TYPE xy<br>
1 0.0993<br>
2 0.0679<br>
3 0.0468<br>
4 0.1339<br>
5 0.0680<br>
6 0.0675<br>
7 0.0141<br>
8 0.1053<br>
9 0.1004<br>
10 0.0966<br>
--------------------------------------------------------------<br>
Can i get a single value for the whole group, except the rmsf values for each atoms in the group?<br>
with regards,<br>
<br>
Moutusi Manna<br>
<br>
<br>
<br></td></tr></table><br>
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