[gmx-users] help with ed sampling
nbesker.cnio at gmail.com
Mon Jan 30 16:43:30 CET 2012
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
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
Why does not the sampling continue up to the target's projection value?
Thanks in advance,
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users