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

Justin Lemkul jalemkul at vt.edu
Fri Apr 17 14:33:01 CEST 2015

On 4/17/15 1:44 AM, Thomas Lipscomb wrote:
> 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:
> /usr/local/gromacs/bin/gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> 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
> /usr/local/gromacs/bin/gmx mdrun -deffnm nvt
> 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)
> /usr/local/gromacs/bin/gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

Your run crashed.

> -------------------------------------------------------
> 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
> -------------------------------------------------------

Thank you for providing all of your files.  This makes it easy to debug. 
Unfortunately for you, you have a litany of serious problems.

1. You're combining the CHARMM27 force field (even though you're calling it 
CHARMM36, which it is not) with Berger UA lipid parameters.  This makes no sense 
at all.  The CHARMM force field fully describes proteins, nucleic acids, lipids, 
etc. with no need to try to augment the force field with external parameters. 
Abort this broken force field.

2. You're getting physical instability because your lipids don't have any bonded 
parameters defined; you've altered ffnonbonded.itp to include lipid interactions 
(DON'T DO THIS) but nothing else.

3. Your configuration is still nonsense, and looks exactly like it did when you 
first reported problems.  You have 24 DPPC lipids scattered randomly in between 
layers of water.  Did you visualize your structure after you built it?  It 
should have been your first indication that something is very wrong.  Your 
protein is effectively surrounded by vacuum with water on either face and a few 
random lipids.  Something went terribly wrong in constructing the system.  Your 
inflated configuration has 125 DPPC; this is normal.  Then, I have no idea what 
you did because what you're calling "system_shrink*.gro" has only DPPC, all 128 
of them.  There's no protein.  Where did it go?  The file "system_solv_ions.gro" 
then shows up with the fragmented structure.  So there's a lot of missing 
information here.  You have magically gone from something sensible (inflated) to 
something very fragmented and unstable :)

4. Energy minimization should have also tipped you off that something is 
horribly wrong:

Potential Energy  = -2.4326836e+05
Maximum force     =  1.1989705e+08 on atom 412
Norm of force     =  1.4800328e+06

Your maximum force is astronomical.  You should have stopped right here to 
investigate what's going on.  It's a combination of (1) junk force field and (2) 
junk configuration.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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