[gmx-users] rmsf question

Tue Mar 16 10:45:53 CET 2010

On Mar 16, 2010, at 10:24 AM, Mark Abraham wrote:

> On 16/03/2010 8:17 PM, XAvier Periole wrote:
>>
>> On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote:
>>
>>> Dear Mark and Tjerk,
>>>
>>> Thank you for your comments.
>>> If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
>>> structure, is a measure of the uncertanty in resolving the  
>>> structure.
>> Well, the "uncertainty of the NMR experiment" would be strongly  
>> correlated
>> with the dynamics of the system in solution, which in a sense  
>> reflects
>> its fluctuations.
>
> ... *if* there's reason to believe that the NMR ensemble reflects  
> the Boltzmann ensemble.
just as much as MD simulations.
> I've no idea how such software works, but I could certainly imagine  
> algorithms that produced a set of plausible structures by varying  
> things that have little or nothing to do with physics... starting  
> points for constrained geometry optimizations, for example.
>
> Mark
>
>> This is different from an actual "uncertainty" of the experiment.
>>> Compared to this the RMSF of C-alpha computed from a MD trajectory
>>> reflects the geometric fluctuations of the backbone in the Boltzmann
>>> distribution of states in the generated ensemble.
>>> The uncertanty in the NMR structure can be influenced by the thermal
>>> fluctuations in the backbone geometry.
>>> Only in this respect the comparison of the two makes sense.
>>> Is this correct?
>>>
>>> Many thanks again for your comments!
>>>
>>> Andrei
>>>
>>> On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham
>>> <Mark.Abraham at anu.edu.au> wrote:
>>>> On 15/03/2010 6:45 PM, Andrei Neamtu wrote:
>>>>>
>>>>> Dear Mark,
>>>>>
>>>>> Thank you very much for your response.
>>>>>
>>>>> What I meant was to obtain a RMSF plot form PDB mediated on each
>>>>> residue and to compare with a RMSF plot mediated on each residue
>>>>> obtained from a MD trajectory.
>>>>> I do not compare a frame from PDB with a frame from MD trajectory.
>>>>
>>>> Sure. I didn't imply you needed or wanted to.
>>>>
>>>> g_rmsf -f your.pdb -s some_suitable.file -n some.ndx
>>>> g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx
>>>>
>>>> In certain cases you'll get to use the same -s or -n, or have to
>>>> juggle atom
>>>> orders.
>>>>
>>>>> So, in the PDB file each 'frame' (MODEL) in the NMR file has the  
>>>>> same
>>>>> order and number of atoms.
>>>>> This is also true for the MD trajectory.
>>>>>
>>>>> In the end i compare the two plots to see if the residues along  
>>>>> the
>>>>> chain have comparable 'flexibility'
>>>>>
>>>>> Is necessary in this case to have a correspondence between the  
>>>>> order
>>>>> of atoms in PDb and in MD trajectory?
>>>>> In this sense the comparison makes sense? (I mean if I do the  
>>>>> residue
>>>>> mediation)
>>>>
>>>> You just need to make sure you are comparing equivalent things. If
>>>> you just
>>>> want (say) a C-alpha RMSF plot, then you can go ahead and do that  
>>>> if the
>>>> index groups work. If you want all-atom RMSF then you might have  
>>>> some
>>>> more
>>>> fiddly work to do.
>>>>
>>>> Mark
>>>>
>>>>> (The PDB is a NMR structure and so it has the hydorgen added and  
>>>>> no
>>>>> missing side chains. And, it has the same number of atoms as the  
>>>>> gro
>>>>> file generated with pdb2gmx. And also the same number of atoms  
>>>>> in the
>>>>> corresponding residues.)
>>>>>
>>>>>
>>>>>
>>>>> Many thanks,
>>>>> Andrei
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham<Mark.Abraham at anu.edu.au 
>>>>> >
>>>>> wrote:
>>>>>>
>>>>>> On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> is there a rapid way to compute RMSF on an NMR ensemble from a  
>>>>>>> PDB
>>>>>>> file?
>>>>>>
>>>>>> Yes, but that's not your problem, it seems :-)
>>>>>>
>>>>>>> g_rmsf needs a .tpr file.
>>>>>>
>>>>>> Not true. Inspect the lines in g_rmsf -h describing the file  
>>>>>> types
>>>>>> suitable
>>>>>> for -f and -s. This is a fairly general GROMACS phenomenon.
>>>>>>
>>>>>>> This is OK with the MD trajectories but if I
>>>>>>> want to compare MD ensemble one with the NMR RMSF ensemble
>>>>>>> fluctuations from the original PDB this is not possible.
>>>>>>
>>>>>> That can be a trickier proposition. You need at least the atom
>>>>>> order to
>>>>>> correspond to make such a comparison.
>>>>>>
>>>>>> If the original atom names are suitable for defining the default
>>>>>> groups,
>>>>>> then you might be in business. Otherwise, you'll need to  
>>>>>> construct
>>>>>> suitable
>>>>>> input for -s (and maybe -n), and see if it matters whether
>>>>>> different atom
>>>>>> names in -f matter.
>>>>>>
>>>>>> Mark
>>>>>> --
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>>
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