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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