Re: [gmx-users] clusterization in dihedral space

2013-01-22 Thread Justin Lemkul 



On 1/22/13 1:17 PM, francesco oteri wrote:

Thank you Mark and Justin,
do you have any reference where this kind of clustering is explained?



What clustering?  I assumed that you had a definition of what you wanted to 
define when you posed the original question.



I mean, since i need a parameter representing the difference between two
frames
to build the matrix, what is the parameter I can use starting from the
dihedrals?



Perhaps you should find a literature example of what you want to do and revisit 
Chapter 8 of the manual, then pose a more direct question.  In order to provide 
you an answer to this question, we need to know (1) what you've done, (2) what 
you're thinking of doing, and (3) what you're actually measuring.  Since we know 
none of these, it's impossible to give any sort of recommendation.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] clusterization in dihedral space

2013-01-22 Thread francesco oteri 
Thank you Mark and Justin,
do you have any reference where this kind of clustering is explained?

I mean, since i need a parameter representing the difference between two
frames
to build the matrix, what is the parameter I can use starting from the
dihedrals?

Francesco



2013/1/22 Mark Abraham 

> On Mon, Jan 21, 2013 at 8:06 PM, francesco oteri
> wrote:
>
> > Thank you,
> > but I don't see how performing cluster analysis with g_angle
> >
>
> g_dih never did do any clustering. As Justin said, g_angle with a suitable
> index group likely does the job for you.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] clusterization in dihedral space

2013-01-22 Thread Mark Abraham 
On Mon, Jan 21, 2013 at 8:06 PM, francesco oteri
wrote:

> Thank you,
> but I don't see how performing cluster analysis with g_angle
>

g_dih never did do any clustering. As Justin said, g_angle with a suitable
index group likely does the job for you.

Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] clusterization in dihedral space

2013-01-21 Thread Justin Lemkul 



On 1/21/13 2:06 PM, francesco oteri wrote:

Thank you,
but I don't see how performing cluster analysis with g_angle



You may have to do some post-processing yourself, but g_angle can certainly 
measure dihedrals and produce distributions.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] clusterization in dihedral space

2013-01-21 Thread francesco oteri 
Thank you,
but I don't see how performing cluster analysis with g_angle

Francesco


2013/1/21 Justin Lemkul 

>
>
> On 1/21/13 1:54 PM, francesco oteri wrote:
>
>> Dear gromacs users,
>> I am trying to run dihedral space clustering with g_dih,
>> but I found that it gives me a lot of error like:
>> Dihedral around 24,26 not found in topology. Using mult=3
>>
>> Looking on the net, I found something alarming: g_dih is gromos specific!
>> http://lists.gromacs.org/**pipermail/gmx-users/2006-**August/023230.html
>>
>> It is still true?
>>
>>
> Yes, and it is for this reason that g_dih has been removed from Gromacs.
>  You can likely accomplish whatever you're trying to do with g_angle.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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/**Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] clusterization in dihedral space

2013-01-21 Thread Justin Lemkul 



On 1/21/13 1:54 PM, francesco oteri wrote:

Dear gromacs users,
I am trying to run dihedral space clustering with g_dih,
but I found that it gives me a lot of error like:
Dihedral around 24,26 not found in topology. Using mult=3

Looking on the net, I found something alarming: g_dih is gromos specific!
http://lists.gromacs.org/pipermail/gmx-users/2006-August/023230.html

It is still true?



Yes, and it is for this reason that g_dih has been removed from Gromacs.  You 
can likely accomplish whatever you're trying to do with g_angle.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists