[gmx-users] Last question: why am I not generating nvt.gro in the KALP15 in DPPC tutorial like last time?

[Thomas Lipscomb]

Dear gmx-users,

Last question because my senior project is ending if a few weeks: why am I not generating nvt.gro this time even though I did in my previous run of the KALP15 in DPPC tutorial and what do I do to fix it?

These are my errors:

FIRST:
/usr/local/gromacs/bin/gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr


ERRORS?:
NOTE 1 [file nvt.mdp, line 48]:
  nvt.mdp did not specify a value for the .mdp option "cutoff-scheme".   Probably it was first intended for use with GROMACS before 4.6. In 4.6,   the Verlet scheme was introduced, but the group scheme was still the   default. The default is now the Verlet scheme, so you will observe   different behaviour.

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.34#

NOTE 2 [file nvt.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note   that with the Verlet scheme, nstlist has no effect on the accuracy of   your simulation.

NOTE 3 [file nvt.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


SECOND:
/usr/local/gromacs/bin/gmx mdrun -deffnm nvt


ERROR:
step 36: Water molecule starting at atom 3649 can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files with previous and current coordinatesSegmentation fault (core dumped)

THIRD:
/usr/local/gromacs/bin/gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

ERROR:
-------------------------------------------------------
Program gmx, VERSION 5.0.1
Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/fileio/futil.cpp, line: 545

File input/output error:
nvt.gro
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


"The coordinate file (-c) is the final output of the NVT simulation."
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html


So I am pretty sure that nvt.gro was supposed to be generated by:
/usr/local/gromacs/bin/gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

or
/usr/local/gromacs/bin/gmx mdrun -deffnm nvt


and used by this part of the NPT calculation, but since no nvt.gro was generated (why?) then this command has the file input/output error for nvt.gro because no nvt.gro was found to input:
/usr/local/gromacs/bin/gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/07_equil2.html



If you need more information, eg. checking the folder to see if I actually did download the file npt.mdp or looking at the readme_KALP_run2.txt file that explains what I did in complete detail, my working directory of all of my stuff is on dropbox (KALP_run2_NPTerrorV2.zip):
https://www.dropbox.com/s/cppibp27vcsnepa/KALP_run2_NPTerrorV2.zip?dl=0


And if you need to compare it to my original (completed but had issues) run, that working directory is also on dropbox (KALP_run1.zip) and also contains a readme_KALP.txt file that explains what I did in complete detail:
https://www.dropbox.com/s/n9nljtycad2qe18/KALP_run1.zip?dl=0


Sincerely,Thomas