Dear Mr Tsjerk Wassenaar :
Thank you for your advice! 
I will try it!
regards!



--- 09年12月23日,周三, Tsjerk Wassenaar <tsje...@gmail.com> 写道:


发件人: Tsjerk Wassenaar <tsje...@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@gromacs.org>
日期: 2009年12月23日,周三,下午7:26


Xi Zhao,

I have no script either. It's not my homework, and I'm not on your payroll. If 
I need a script like that and write it, I'll be happy to share it with you. But 
that's not going to be soon. At present, I don't even have a data set to use to 
develop something like it. On the other hand, if you put effort in writing a 
script for it (you may want to try and learn a bit of python), and get stuck, 
I'll be happy to reflect on your code, as will others that are on this list. 
That is how things work here.

Cheers,

Tsjerk


On Wed, Dec 23, 2009 at 2:07 AM, xi zhao <zhaoxiitc2...@yahoo.com.cn> wrote:









Dear Mr Tsjerk Wassenaar : 
Thank you for your help!
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 <tsje...@gmail.com> 写道:



发件人: Tsjerk Wassenaar <tsje...@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@gromacs.org>
日期: 2009年12月22日,周二,下午7:43





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 <zhaoxiitc2...@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! 




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


发件人: Tsjerk Wassenaar <tsje...@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@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 <zhaoxiitc2...@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!





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Neuropharmacologist


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Medicinal Chemist
Neuropharmacologist


-----下面为附件内容-----


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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist


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