[gmx-users] rmsf question

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 14 14:16:46 CET 2010

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.


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