[gmx-users] problem with g_rmsf

Adriana Pietropaolo adriana at ms.fci.unibo.it
Mon Feb 13 11:58:35 CET 2006

Hi gromacs users,
I've posted last friday, but I didn't have an answer about my doubt.
I've not well understand how g_rmsf makes the least squares respect to a 
reference structure.
If I make:
g_rmsf -f a.xtc -s a.tpr -q standard.pdb -od
where a.tpr is the run file relative to the xtc trajectory,
I don't know why if I change the standard pdb, with a run 
configuration, the results is the same, I thought that this part of the 
protein is very rigid, but if I make:
g_rmsf -f a.pdb -s a.tpr -q a.pdb
where the reference and input configurations are the same and a.pdb is one 
the results is different from zero.
So I have a doubt that I' m falling in something, or I bad understand 
Somebody can help me?

Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
Tel 051/6446992
FAX 051/2093690 

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