[gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Dec 21 12:57:33 CET 2009

Ni hao,

Since it's a projection, there is not (in general) a single conformation for
each point in the 2D plane. On the other hand, the points you obtained are
derived from distinct (ordered) conformations, so it is trivial to retrieve
them. Each conformation (time) yields one point: find the time for which the
point corresponds with the one your interested in, and extract the
conformation from the trajectory.



2009/12/20 xi zhao <zhaoxiitc2002 at yahoo.com.cn>

> Dear users for gromacs:
> We know that observing the sampled conformations in the subspace spanned
> by the eigenvectors is a so-called two-dimensional projection(2D
> projection), in 2-D projection, each point represents a snapshot from
> the simulation, and the distribution shows the sampled region along the
> first two eigenvectors during the simulation. But I feel confounded,
> because I do not know to how to obtain corresponding conformation for
> each point in the 2-D projection.Please help me!
> best regards!
> thank you!
> [image: 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
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