[gmx-users] g_cluster warning

[Mark Abraham]

Thanks for the report Sabine.

It would be nice if the original reporters could take the extra 5 seconds
to copy-paste and report the command lines they used. There are way too
many things that they or GROMACS could be doing wrong for any of us to
spend time guessing what is going on. :-)

Mark


On Wed, May 15, 2013 at 4:54 PM, Sabine Reisser <sabine.reisser at kit.edu>wrote:

> Hi,
>
> by looking into the code I could figure out some things.
>
>
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
>
> This warning comes from the -rmsmin option which is set to 0 by default
> and which controls the structure output.
>
> The problem with tpr/gro files is that g_cluster uses mass weighted RMSD
> calculation by default and if there are no masses (as in the gro file), it
> tries to assign masses from the atom name. This lead to masses of around
> 200 for H atoms which are called HG*, the program assumed this was mercury!
>
> So I'd strongly advise everybody to use tpr files within g_cluster. It
> would also be nice to insert a warning in g_cluster if atoms other than C,
> O, N, H, S are "found".
>
> Cheers
> Sabine
>
>
>
>
> On 05/14/2013 06:06 PM, Mark Abraham wrote:
>
>> Hi,
>>
>> I don't know. I don't know how to trigger it, and nobody has said how they
>> triggered it :-)
>>
>> Mark
>> On May 14, 2013 4:45 PM, "Preeti Choudhary" <
>> preetichoudhary18111989 at gmail.**com <preetichoudhary18111989 at gmail.com>>
>> wrote:
>>
>>  should we worry about the warning ???
>>>
>>>
>>> On Tue, May 14, 2013 at 7:19 PM, Mark Abraham <mark.j.abraham at gmail.com
>>>
>>>> wrote:
>>>> We'd need a lot more info to start to understand why .tpr vs .gro
>>>> does/should affect the result (or not)!
>>>>
>>>> Mark
>>>> On May 14, 2013 2:32 PM, "Sabine Reisser" <sabine.reisser at kit.edu>
>>>>
>>> wrote:
>>>
>>>> Hi,
>>>>>
>>>>> I'm having the same warning, would also be interested in what it means.
>>>>>
>>>>> Additionally, I get different results if I use a tpr instead of a gro
>>>>>
>>>> file
>>>>
>>>>> in the -s option, using the same trajectory with -f. The results are
>>>>> completely different, for the gro file I get 42 while for the tpr file
>>>>>
>>>> I
>>>
>>>> get 2 clusters.
>>>>>
>>>>> Does anybody know why this is the case?
>>>>>
>>>>> Cheers
>>>>> Sabine
>>>>>
>>>>>
>>>>>
>>>>> On 05/10/2013 04:33 PM, Preeti Choudhary wrote:
>>>>>
>>>>>  hello everyone
>>>>>>
>>>>>> I am trying to cluster my data using g_cluster.I simulated the whole
>>>>>> protein. I did the g_cluster analysis with only certain region of the
>>>>>> protein which I specified using an index file.The program runs fine
>>>>>>
>>>>> and
>>>
>>>> gives 1 cluster.My concern is the warning it gives which states that
>>>>>>
>>>>> :-
>>>
>>>> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
>>>>>>
>>>>>>
>>>>>> what exactly this warning means ???
>>>>>>
>>>>>> -thanks
>>>>>>
>>>>>>  --
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