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

xi zhao zhaoxiitc2002 at yahoo.com.cn
Wed Dec 23 02:07:54 CET 2009

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Dear Mr Tsjerk Wassenaar :
I only study on conformation transfromation (transformation) of protein, and need point to corresponding conformation in 2d projection or free energy landscape! I have no any script, please help me!
Best regards!

--- 09年12月22日，周二, Tsjerk Wassenaar <tsjerkw at gmail.com> 写道：

Ni hao Xi Zhao,

Please note again that you're working with projections. There is not necessarily a single conformation that corresponds to the energy minimum from your projection space.
You can obtain the minimum from the 2D projection and then find the conformation that yields the projection closest to that point, by taking the Euclidean distance between the projection and the minimum. You'll have to do a bit of scripting there.

Cheers,

Tsjerk

On Mon, Dec 21, 2009 at 2:51 PM, xi zhao <zhaoxiitc2002 at yahoo.com.cn> wrote:

Dear Mr Tsjerk Wassenaar ：
what you said is reasonal, but how to implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the  minimum of energy surface?
best regards!

--- 09年12月21日，周一, Tsjerk Wassenaar <tsjerkw at gmail.com> 写道：

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.

Cheers,

Tsjerk

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
best regards!
thank you!

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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist

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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist

-----下面为附件内容-----

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