Hi,<div><br></div><div>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:</div>
<div><br></div><div><div># This file was created Sat Jul 17 13:40:21 2010</div><div># by the following command:</div><div># ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res</div>
<div>#</div><div># g_rmsf is part of G R O M A C S:</div><div>#</div><div># GROup of MAchos and Cynical Suckers</div><div>#</div><div>@ title "RMS fluctuation"</div><div>@ xaxis label "Residue"</div>
<div>@ yaxis label "(nm)"</div><div>@TYPE xy</div><div> 1 nan</div><div> 2 nan</div><div> 3 0.0002</div><div> 4 0.0000</div><div> 5 nan</div><div> 1 0.0002</div><div> 2 nan</div>
<div> 3 nan</div><div> 4 0.0001</div><div> 5 nan</div><div> 6 0.0001</div><div> 7 nan</div><div> 8 nan</div><div> 9 0.0000</div><div> 10 0.0002</div><div> 11 nan</div>
<div> 12 nan</div><div> 13 nan</div><div> 14 nan</div><div> 15 0.0000</div><div> 16 nan</div><div> 17 0.0001</div><div> 18 0.0002</div><div><br></div>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?</div>
<div><br></div><div>Pooja<br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
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