Hi everybody,<div><br></div><div>I am trying to do essential dynamics sampling from a starting structure to the target structure, so I am using the command:</div><div><br></div><div>make_edi_d -f ../eigenvec.trr -eig ../eigenval.xvg -s topol.tpr -radcon "1" -n index.ndx -tar target.gro</div>
<div><br></div><div>The projection of the starting structure and of the target structure on the first eigenvector is 3.5 and -2.8, respectively </div><div>(I double checked the projection of these structures on the first eigenvector). </div>
<div>However, the sam.edo shows that after about 5000 steps the sampling is "constrained" at a value of the projection of 2.4 and the contracting radius becomes 0 (the initial value of the contracting radius is 1.1).</div>
<div>If I give two first eigenvectors instead of the first one:</div><div>make_edi_d -f ../eigenvec.trr -eig ../eigenval.xvg -s topol.tpr -radcon "1-2" -n index.ndx -tar target.gro</div><div><br></div><div>in the sam.edo file the contracting radius starts from 2.2 and the sampling "stops" at the same point as before. </div>
<div>I do not understand. Can I chose the initial value of the contracting radius? </div><div>Why does not the sampling continue up to the target's projection value?</div><div>Thanks in advance,</div><div><br></div><div>
Neva</div>