[gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

[ms]

On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
> H Massimo,
>
> The RMSD over time is the RMSD against a single reference structure. For
> clustering you use the RMSD matrix, which has all pairwise RMSDs. The
> distribution you show is the distribution of RMSD values in that matrix.
Aha! This makes much more sense then, thanks!
Is there a Gromacs command to get the histogram of RMSD against a single 
reference structure, then?

thanks,
Massimo

> Cheers,
>
> Tsjerk
>
>
>
> On Wed, Aug 13, 2014 at 3:44 PM, ms <devicerandom at gmail.com> wrote:
>
>> Hi Tsjerk,
>>
>>
>> On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote:
>>
>>> You have two clusters, both with low within-cluster RMSD. This shows up as
>>> the first peak in the RMSD distribution. The second peak is the
>>> between-clusters RMSD.
>>>
>> I am sorry, but I don't understand anything here - what does
>> "within-cluster RMSD" means? what is the "between-clusters RMSD"?
>>
>> I would expect the RMSD distribution to mirror the RMSD vs time plot ;
>> that is, if I take the points from the rmsd-time.xvg and I make an
>> histogram, I would expect to recover the RMSD distribution. Am I wrong?
>>
>> thanks a lot for your help,
>>
>> m.
>>
>>   Cheers,
>>> Tsjerk
>>>
>>>
>>>
>>> On Wed, Aug 13, 2014 at 3:14 PM, ms <devicerandom at gmail.com> wrote:
>>>
>>>   Dear Gromacs users,
>>>> I am analyzing the RMSD evolution of a trajectory with g_rms and
>>>> clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing
>>>> something
>>>> quite odd in the RMSD distribution. I link here the RMSD evolution over
>>>> time , the cluster ID over time, and the RMSD distribution (see
>>>> http://imgur.com/a/0ftA2 ).
>>>>
>>>> RMSD evolution in time and cluster ID in time seem to make sense -the
>>>> larger cluster is cluster 1, and it indeed populates most of the
>>>> trajectory.
>>>>
>>>> The RMSD distribution is also correctly bimodal and peaked around the
>>>> right values, at least visually. However, I would expect that the peak
>>>> around 0.3-0.4 should be larger than the peak around 0.1, given the time
>>>> evolution/distribution of RMSD, yet I see the opposite, apparently. What
>>>> does it mean?
>>>>
>>>> Thanks,
>>>> Massimo
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