Dear tsjerk,<div><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: medium; white-space: pre; "><br></span></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; ">I am very sorry to say that your suggestions does not help but increase confusions only. I am highly obliged if you give me clear statements about the scores to understand this concept in depth. I have searched</span> <span class="Apple-style-span" style="white-space: pre; ">research article about this concept but failed to find even an single article. Neither Gromacs tutorial give any description about these scores, nor your PCA tutorial. I am really interested to understand this concept so help by giving me answers of my questions.</span></font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: normal; "><pre>eigenvector Minimum Maximum
value time value time
1 -9.162661 99.0 2.682097 9450.0
2 -2.728093 4695.0 3.272116 558.0</pre></span></span></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><br></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3">I got clearcut idea about this line after read your tutorial "</font><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><b>These are the maximum and minimum projections on the eigenvectors."</b> </span></font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><br></span></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; ">What is the meaning of this line here? <b>"They are very unlikely to correspond to energy minima, as minima will be modal."</b></span></font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><br></span></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; ">If the values in second column not the energy values they are scores only.</span><b style="white-space: pre; "> </b><span class="Apple-style-span" style="white-space: pre; ">Are scores directly corresponds to the energy minima for second column and energy maxima for 4th column on which they are based? I have seen that in second column there are negative values (Minimum) and in 4th column there are positive values (Maximum). In above example along the first eigenvector, Are -9.162661 value at time 99 ps corresponding to the structure at low energy during the projection and the value 2.682097 score corresponds to the maximum energy. If I am wrong then tell me, what are the criteria on which there scores are based? </span></font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><br></span></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; ">I am totally agree with your this concept and understand completely in this line <b>"Think of a pendulum, projecting the position on the floor."</b> </span></font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; "><br></span></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3"><span class="Apple-style-span" style="white-space: pre; ">But this statement confused me <b>"The extreme projections actually correspond to states of higher (potential) energy"</b>. Which extreme projection corresponds to state of higher (potential) energy either minimum or maximum or both of them?</span></font></div>
<div><br></div><div>Please reply me line by line so that I can understand this concept.</div><br>-- <br>Pawan Kumar Raghav<br>Bioinformatician<br>