[gmx-users] rmsf question
Mark.Abraham at anu.edu.au
Sun Mar 14 14:16:46 CET 2010
On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
> 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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