Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this?<div> "With the option -od the root mean square deviation with respect to the reference structure is calculated"</div>
<div>What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory?</div><div><br></div><div>Thanks!<br clear="all"><br><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">>Pan Wu wrote:<br>
>> Hi everyone,<br>>> Thank you for answering my former questions, it really help me, the<br>>> new gmx-er a lot~<br>>> Here is another question about reference state of <span class="il" style="background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: rgb(255, 255, 136); background-position: initial initial; ">RMSF</span>.<br>
>> In the manual, it shows "g_rmsf computes the root mean square<br>>> fluctuation (<span class="il" style="background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: rgb(255, 255, 136); background-position: initial initial; ">RMSF</span>, i.e. standard deviation) of atomic positions<br>
>> after (optionally) fitting to a reference frame". So in this way, can I<br>>> choose the reference frame from *.tpr file or the coordinate average<br>>> over the whole trajectory? If Gromacs can, how?<br>
><br>>I believe the reference structure is taken from whatever structure file is given<br>>to the -s flag, so in principle you could provide any frame from the trajectory,<br>>as well as the initial one, or some average structure (from, i.e. g_cluster or<br>
>something similar).<br>><br>>-Justin<br></span>
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