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!
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-----
--
gmx-users mailing list gmx-users@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
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-----
--
gmx-users mailing list gmx-users@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
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-----
--
gmx-users mailing list gmx-users@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
___________________________________________________________
好玩贺卡等你发,邮箱贺卡全新上线!
http://card.mail.cn.yahoo.com/
--
gmx-users mailing list gmx-users@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