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

Wed Dec 23 14:36:35 CET 2009

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

--- 09年12月23日，周三, 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 <zhaoxiitc2002 at 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 <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 <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! 

--- 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>

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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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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