[gmx-users] g_rmsf

[Sai Pooja]

Hi,

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
set?

Pooja
-- 
Quaerendo Invenietis-Seek and you shall discover.
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