[gmx-users] rmsf question

[Tsjerk Wassenaar]

Hi Andrei,

You can do it this way. But do mind that the ensemble from NMR is not
meant to reflect the Boltzmann distribution. Rather it is meant to
provide a number of plausible solutions given the (positive)
restraints from the experiments and the force field used for the
refinement. This means that the moments of the distribution (mean and
fluctuation) need not be comparable quantitatively. A more direct
comparison between experiments and simulations could be obtained by
comparing backbone order parameters.

Cheers,

Tsjerk

On Mon, Mar 15, 2010 at 8:45 AM, Andrei Neamtu <neamtuandrei at gmail.com> 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.
> 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)
>
> (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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist