Hi Pooja, 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.
Cheers, Tsjerk On Sat, Jul 17, 2010 at 7:55 PM, Sai Pooja <saipo...@gmail.com> wrote: > 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. > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php