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

[Tsjerk Wassenaar]

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 ：*
> *Thank you for your help! *
> *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!
>
>
> [image: 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *09年12月21日，周一, Tsjerk Wassenaar <tsjerkw at gmail.com>* 写道：
>
>
> 发件人: Tsjerk Wassenaar <tsjerkw at gmail.com>
> 主题: Re: [gmx-users] how to obtain corresponding conformation for each point
> in the 2-D projection
> 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> 日期: 2009年12月21日,周一,下午7:57
>
>
> 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<http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@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
> Neuropharmacologist
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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