[gmx-users] g_rmsf over time windows

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 8 08:58:38 CEST 2008

Hi Giordano,

Do you have a conformational change? If you consider unidirectional
motion, in one or N coordinates alike, you would expect just what you
see for the fluctuations. In fact, it's not really fluctuation then.
10 ns is also pretty short for a simulation of a protein. It's likely
that you're analyzing relaxation from the starting structure.



On Tue, Oct 7, 2008 at 8:03 PM, giordano mancini
<baloilgiullare at interfree.it> wrote:
> Hi all,
> I have the following problem: I have a simulation
> of 10 ns of a protein in water. I have extracted the protein trajectory
> with trjconv -pbc nojump and the fitted it to a reference structure
> with trjconv -fit rot+trans.
> If I run g_rmsf -nofit over two consecutive chunks of 5 ns i get very
> similar rmsf values (so the fluctuations are are the same in the 2 time
> windows). However if I run g_rmsf over the whole trajectory i get much
> higher values of rmsf (up to 0.1 - 0.15 nm). The difference become higher if
> use 4 windows of 2.5 ns each (i.e. the rmsf over 2.5 ns are smaller).
> I think there's something wrong with the reference structure which is
> different in the various cases so that with shorter trajectories the std
> dev is smaller; however I always use the same .gro (or tpr). May be are
> the -b and -e flags?
> Use of tpr/gro reference, fit with g_rmsf, calpha or backbone,
> or -res option does not change things.
> I have tried with gromacs 3.3.1 and 3.3.3
> Here 's my complete syntax:
> $> trjconv -s box.gro -f nojump.xtc -n index.ndx -o nj -pbc nojump
> $> trjconv -s box.gro -f nj.xtc -n index -fit rot+trans -o fitted
> $> g_rmsf -s box.gro -f fitted -n index -o rmsf$start -b $start -e $end
> for chuncks
> $> g_rmsf -s box.gro -f fitted -n index -o rmsf
> thanks for your help
> giordnao mancini
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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