Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread bipin singh 
Now got the point. Thank you Tsjerk Sir and Prof. David for the help.


On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar  wrote:

> Hi Bipin,
>
> If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll
> end up in the same cluster.
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, Jul 31, 2013 at 9:45 AM, bipin singh  wrote:
>
> > Thanks for the reply Prof. David. But in the output it shows that "The
> RMSD
> > ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
> > me. So I think it should write the snapshots having RMSD greater than
> 0.3nm
> > (cutoff) to another cluster.
> >
> >
> > On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
> > wrote:
> >
> > > On 2013-07-31 07:20, bipin singh wrote:
> > >
> > >> Hello All,
> > >>
> > >> I was trying to do clustering on my MD trajectory using gromos method
> > >> under
> > >> g_cluster module. I got one doubt regarding the output, as I used the
> > >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
> > >> snapshots which have RMSD less than or equal to 0.3nm will form the
> > first
> > >> cluster and the rest of snapshots will form another cluster. But the
> > >> output
> > >> gives a single cluster. Please let me know if I have not understood it
> > >> correctly.
> > >>
> > >
> > > It means everything is within 0.3 nm RMSD from each other. Maybe your
> > > system is very stable or you did not simulate very long. You can use a
> > > shorter cut-off.
> > >
> > >
> > >> I am appending the output below:
> > >>
> > >> ##**##
> > >> Using gromos method for clustering
> > >> Using RMSD cutoff 0.3 nm
> > >> The RMSD ranges from 0.0602553 to 0.411066 nm
> > >> Average RMSD is 0.107366
> > >> Number of structures for matrix 12501
> > >> Energy of the matrix is 960.075 nm
> > >>
> > >> Found 1 clusters
> > >>
> > >> Writing middle structure for each cluster to clusters.pdb
> > >> Counted 0 transitions in total, max 0 between two specific clusters
> > >> ##**
> > >>
> > >>
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Dept. of Cell & Molec. Biol., Uppsala University.
> > > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > * Please search the archive at http://www.gromacs.org/**
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> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> > http://www.gromacs.org/Support/Mailing_Lists>
> > >
> >
> >
> >
> > --
> > *---
> > Thanks and Regards,
> > Bipin Singh*
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
*---
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread Tsjerk Wassenaar 
Hi Bipin,

If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll
end up in the same cluster.

Cheers,

Tsjerk


On Wed, Jul 31, 2013 at 9:45 AM, bipin singh  wrote:

> Thanks for the reply Prof. David. But in the output it shows that "The RMSD
> ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
> me. So I think it should write the snapshots having RMSD greater than 0.3nm
> (cutoff) to another cluster.
>
>
> On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
> wrote:
>
> > On 2013-07-31 07:20, bipin singh wrote:
> >
> >> Hello All,
> >>
> >> I was trying to do clustering on my MD trajectory using gromos method
> >> under
> >> g_cluster module. I got one doubt regarding the output, as I used the
> >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
> >> snapshots which have RMSD less than or equal to 0.3nm will form the
> first
> >> cluster and the rest of snapshots will form another cluster. But the
> >> output
> >> gives a single cluster. Please let me know if I have not understood it
> >> correctly.
> >>
> >
> > It means everything is within 0.3 nm RMSD from each other. Maybe your
> > system is very stable or you did not simulate very long. You can use a
> > shorter cut-off.
> >
> >
> >> I am appending the output below:
> >>
> >> ##**##
> >> Using gromos method for clustering
> >> Using RMSD cutoff 0.3 nm
> >> The RMSD ranges from 0.0602553 to 0.411066 nm
> >> Average RMSD is 0.107366
> >> Number of structures for matrix 12501
> >> Energy of the matrix is 960.075 nm
> >>
> >> Found 1 clusters
> >>
> >> Writing middle structure for each cluster to clusters.pdb
> >> Counted 0 transitions in total, max 0 between two specific clusters
> >> ##**
> >>
> >>
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> 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<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>
>
> --
> *---
> Thanks and Regards,
> Bipin Singh*
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread David van der Spoel 

On 2013-07-31 09:45, bipin singh wrote:

Thanks for the reply Prof. David. But in the output it shows that "The RMSD
ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.
I see, then maybe the definition is different (check the source code!). 
It could be that it is 0.3 nm from the cluster center.



On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
wrote:


On 2013-07-31 07:20, bipin singh wrote:


Hello All,

I was trying to do clustering on my MD trajectory using gromos method
under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the
output
gives a single cluster. Please let me know if I have not understood it
correctly.



It means everything is within 0.3 nm RMSD from each other. Maybe your
system is very stable or you did not simulate very long. You can use a
shorter cut-off.



I am appending the output below:

##**##
Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
##**




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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!
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread bipin singh 
Thanks for the reply Prof. David. But in the output it shows that "The RMSD
ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.


On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
wrote:

> On 2013-07-31 07:20, bipin singh wrote:
>
>> Hello All,
>>
>> I was trying to do clustering on my MD trajectory using gromos method
>> under
>> g_cluster module. I got one doubt regarding the output, as I used the
>> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
>> snapshots which have RMSD less than or equal to 0.3nm will form the first
>> cluster and the rest of snapshots will form another cluster. But the
>> output
>> gives a single cluster. Please let me know if I have not understood it
>> correctly.
>>
>
> It means everything is within 0.3 nm RMSD from each other. Maybe your
> system is very stable or you did not simulate very long. You can use a
> shorter cut-off.
>
>
>> I am appending the output below:
>>
>> ##**##
>> Using gromos method for clustering
>> Using RMSD cutoff 0.3 nm
>> The RMSD ranges from 0.0602553 to 0.411066 nm
>> Average RMSD is 0.107366
>> Number of structures for matrix 12501
>> Energy of the matrix is 960.075 nm
>>
>> Found 1 clusters
>>
>> Writing middle structure for each cluster to clusters.pdb
>> Counted 0 transitions in total, max 0 between two specific clusters
>> ##**
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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
>



-- 
*---
Thanks and Regards,
Bipin Singh*
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread David van der Spoel 

On 2013-07-31 07:20, bipin singh wrote:

Hello All,

I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the output
gives a single cluster. Please let me know if I have not understood it
correctly.


It means everything is within 0.3 nm RMSD from each other. Maybe your 
system is very stable or you did not simulate very long. You can use a 
shorter cut-off.


I am appending the output below:


Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
##




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Regarding gromos method in g_cluster

2013-07-30 Thread bipin singh 
Hello All,

I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the output
gives a single cluster. Please let me know if I have not understood it
correctly.

I am appending the output below:


Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
##

-- 
*---
Thanks and Regards,
Bipin Singh*
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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