[gmx-users] KALP15 in DPPC: NPT: File input/output error: nvt.gro

Thomas Lipscomb linuxborg2 at yahoo.com
Thu Apr 2 23:11:16 CEST 2015

Dear gmx-users,
Ok I figured out the lipid packing from my previous questionhttps://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096396.html
 But now when I am at this NPT step:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/07_equil2.html
/usr/local/gromacs/bin/gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
I get this error I do not know how to fix:
-------------------------------------------------------Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/fileio/futil.cpp, line: 545
File input/output error:nvt.groFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------

I am also worried that before then, at the end of my NVT the temperature did not stabilize, because:
/usr/local/gromacs/bin/gmx energy

T-rest32 Last energy frame read 13 time   17.000           
Statistics over 18 steps [ 0.0000 through 17.0000 ps ], 1 data setsAll statistics are over 14 points (frames)
Energy                      Average   Err.Est.       RMSD  Tot-Drift-------------------------------------------------------------------------------T-rest                            0          0          0          0  (K)
For a step-by-step procedure of what I did, see readme_KALP_run2.txt in my working directory here:https://www.dropbox.com/s/cppibp27vcsnepa/KALP_run2_NPTerrorV2.zip?dl=0
That working directory also contains all of my files, eg. topol.top

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