[gmx-users] Regarding gromos method in g_cluster

[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
<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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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*