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

2009-12-23 Thread xi zhao 

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



--- 09年12月23日，周三, Tsjerk Wassenaar  写道：


发件人: Tsjerk Wassenaar 
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" 
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  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  写道：



发件人: Tsjerk Wassenaar 
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" 
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  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  写道：


发件人: Tsjerk Wassenaar 
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" 
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 





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!





好玩贺卡等你发，邮箱贺卡全新上线！
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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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist


-下面为附件内容-


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

2009-12-23 Thread Tsjerk Wassenaar 
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  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!
>
> [image: 
> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *09年12月22日，周二, Tsjerk Wassenaar * 写道：
>
>
> 发件人: Tsjerk Wassenaar 
> 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" 
> 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 
> http://cn.mc151.mail.yahoo.com/mc/compose?to=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!
>>
>>
>> [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 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=tsje...@gmail.com>
>> >* 写道：
>>
>>
>> 发件人: Tsjerk Wassenaar 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=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" 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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 
>> http://cn.mc151.mail.yahoo.com/mc/compose?to=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!
>>>
>>>
>>> [image: 
>>> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>> --
>>> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>>> --
>>> gmx-users mailing list
>>> gmx-users@gromacs.org<http://cn.mc151.mail.yahoo.c

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

2009-12-22 Thread xi zhao 


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  写道：


发件人: Tsjerk Wassenaar 
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" 
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  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  写道：


发件人: Tsjerk Wassenaar 
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" 
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 





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!





好玩贺卡等你发，邮箱贺卡全新上线！
--
gmx-users mailing list    gmx-us...@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist


-下面为附件内容-


-- 

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

2009-12-22 Thread 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  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 * 写道：
>
>
> 发件人: Tsjerk Wassenaar 
> 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" 
> 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 
> http://cn.mc151.mail.yahoo.com/mc/compose?to=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!
>>
>>
>> [image: 
>> 4]<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>> --
>> 好玩贺卡等你发，邮箱贺卡全新上线！<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>> --
>> gmx-users mailing list
>> gmx-users@gromacs.org<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to 
>> gmx-users-requ...@gromacs.org<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>
>> .
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
>
> -下面为附件内容-
>
> --
> gmx-users mailing list
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> .
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

2009-12-21 Thread xi zhao 
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  写道：


发件人: Tsjerk Wassenaar 
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" 
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 





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!





好玩贺卡等你发，邮箱贺卡全新上线！
--
gmx-users mailing list    gmx-us...@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist


-下面为附件内容-


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

2009-12-21 Thread Tsjerk Wassenaar 
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 

> 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]
> --
> 好玩贺卡等你发，邮箱贺卡全新上线！
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-- 
Tsjerk A. Wassenaar, Ph.D.

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

2009-12-19 Thread xi zhao 
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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