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