[gmx-users] Regarding gromos method in g_cluster

[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
> <spoel at xray.bmc.uu.se>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.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se