tsjerkw at gmail.com
Sat Jul 17 21:33:41 CEST 2010
Try to get a grip on the file types and what they contain. A .cpt file
is a checkpoint file containing a single configuration. Not much
fluctuation to expect there. This sort of analysis only makes sense
for a trajectory, or at least an ensemble of structures. Try the .xtc
or the .trr file.
On Sat, Jul 17, 2010 at 7:55 PM, Sai Pooja <saipooja at gmail.com> wrote:
> I am running an npt simulation for a protein in water. For more than 50% of
> the residues the backbone atoms have been restrained by applying
> posrestraints. I ran g_rmsf to check if the pos-restraints were working
> well. When I do this selecting 'backbone' from the groups menu, my rmsf file
> gives 'nan' for certain residues:
> # This file was created Sat Jul 17 13:40:21 2010
> # by the following command:
> # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o
> rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res
> # g_rmsf is part of G R O M A C S:
> # GROup of MAchos and Cynical Suckers
> @ title "RMS fluctuation"
> @ xaxis label "Residue"
> @ yaxis label "(nm)"
> @TYPE xy
> 1 nan
> 2 nan
> 3 0.0002
> 4 0.0000
> 5 nan
> 1 0.0002
> 2 nan
> 3 nan
> 4 0.0001
> 5 nan
> 6 0.0001
> 7 nan
> 8 nan
> 9 0.0000
> 10 0.0002
> 11 nan
> 12 nan
> 13 nan
> 14 nan
> 15 0.0000
> 16 nan
> 17 0.0001
> 18 0.0002
> Does this mean that the simulations are not working properly? Does this
> problem occur frequently due to the way the simulation parameters haev been
> Quaerendo Invenietis-Seek and you shall discover.
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Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
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