[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 2 00:50:57 CEST 2019 

Hi,

What does ls -l return when run from your working directory?

Mark

On Fri, 2 Aug 2019 at 01:49, Mohammed I Sorour <Mohammed.Sorour at temple.edu>
wrote:

> Hello Dr. Dallas,
>
> Yes, the nvt.tpr was created and I had it in the local directory ready for
> the mdrun.
> Yes, those copy/pastes of the commands I used.
> Since I'm kind of new to the MD simulations, so I'm sticking to that
> tutorial
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> .
> Also, I tried to use the mdrun command in a different way just to give it a
> try
>
> command: gmx mdrun -s nvt.tpr -deffnm nvt
>
> It gave me the following error.
>
> Error in user input:
> Invalid command-line options
>   In command-line option -s
>     File 'nvt.tpr' does not exist or is not accessible.
>     The file could not be opened.
>       Reason: No such file or directory
>       (call to fopen() returned error code 2)
>
> I know that it is clearly saying that nvt.tpr is not there. But I'm also
> sure that I have it there.
>
> Thanks,
> Mohammed
>
> On Thu, Aug 1, 2019 at 6:40 PM Dallas Warren <dallas.warren at monash.edu>
> wrote:
>
> > From that command, was the nvt.tpr actually created? Can you see it in
> the
> > directory? What happens if you type in the files for each of the command
> > switches instead of using -deffnm to autocomplete them for you?
> >
> > Are those copy/pastes of the commands you used?
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.warren at monash.edu
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble
> a
> > nail.
> >
> >
> > On Fri, 2 Aug 2019 at 08:30, Mohammed I Sorour <
> Mohammed.Sorour at temple.edu
> > >
> > wrote:
> >
> > > Hi Justin,
> > >
> > >  Thank you so much for your reply.
> > >
> > > for the NVT run, I used the following commands
> > >
> > > *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*
> > >
> > > which generated the nvt.tpr file and printed the following:
> > >
> > > Ignoring obsolete mdp entry 'title'
> > >
> > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> > > Setting the LD random seed to 708625668
> > > Generated 4851 of the 4851 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 0.5
> > > Generated 4851 of the 4851 1-4 parameter combinations
> > > Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> > > turning all bonds into constraints...
> > > Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
> > > turning all bonds into constraints...
> > > Excluding 2 bonded neighbours molecule type 'SOL'
> > > turning all bonds into constraints...
> > > Excluding 1 bonded neighbours molecule type 'MG'
> > > turning all bonds into constraints...
> > > Excluding 1 bonded neighbours molecule type 'CL'
> > > turning all bonds into constraints...
> > >
> > > NOTE 1 [file topol.top, line 51]:
> > >   System has non-zero total charge: -117.999968
> > >   Total charge should normally be an integer. See
> > >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >   for discussion on how close it should be to an integer.
> > >
> > >
> > >
> > > Setting gen_seed to -1290262031
> > > Velocities were taken from a Maxwell distribution at 300 K
> > > Removing all charge groups because cutoff-scheme=Verlet
> > > Analysing residue names:
> > > There are:   124        DNA residues
> > > There are: 455308      Water residues
> > > Number of degrees of freedom in T-Coupling group DNA is 7631.99
> > > Number of degrees of freedom in T-Coupling group Water is 2724393.00
> > > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
> > > Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036
> nm
> > > Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000
> nm
> > > Note that mdrun will redetermine rlist based on the actual pair-list
> > setup
> > > Calculating fourier grid dimensions for X Y Z
> > > Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150
> > > Estimate for the relative computational load of the PME mesh part: 0.16
> > >
> > > NOTE 2 [file nvt.mdp]:
> > >   This run will generate roughly 31380 Mb of data
> > >
> > >
> > > There were 2 notes
> > >
> > > GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)
> > >
> > > *Then I used the mdrun command *
> > >
> > > *gmx mdrun -deffnm nvt*
> > >
> > >
> > >
> > > Again, I have run a couple of systems before that and I successfully
> ran
> > > the MD_production calculation, following the same procedure. The only
> > > difference I could notice is the charges rounding, because it didn't
> > happen
> > > with those that ran successfully. That is why I suspected that.
> > >
> > > Please, let me know if I need to provide more information.
> > >
> > > Thanks,
> > >
> > > Mohammed
> > >
> > >
> > > On Thu, Aug 1, 2019 at 3:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > > >
> > > >
> > > > On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
> > > > > Dear Gromacs users,
> > > > >
> > > > > I'm running MD simulation on a couple of DNA systems that only vary
> > in
> > > > > sequence. Most of the runs worked just fine, but surprisingly I
> have
> > > one
> > > > > system that I got an error in the NVT equilibration step.
> > > > > I'm following the
> > > > > tutorialhttp://
> > > >
> > >
> >
> www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> > > > >
> > > > > rogram:     gmx mdrun, version 2016.3
> > > > > Source file: src/gromacs/options/options.cpp (line 258)
> > > > > Function:    void gmx::Options::finish()
> > > > >
> > > > > Error in user input:
> > > > > Invalid input values
> > > > >    In option s
> > > > >      Required option was not provided, and the default file 'topol'
> > > does
> > > > not
> > > > >      exist or is not accessible.
> > > > >      The following extensions were tried to complete the file name:
> > > > >        .tpr
> > > > >
> > > > > I'm pretty sure that I have the .tpr  files in the local
> directory. I
> > > > have
> > > > > read the previous reviews of the Gromacs mailing list, and I know
> > that
> > > > > it would be a problem with the toplogy file. The toplogy files
> looks
> > > > > so far good to me.
> > > >
> > > > There's a typo in your command or the input file you think is there
> is
> > > > not. You didn't provide your mdrun command (please always do this)
> but
> > I
> > > > suspect the former. If mdrun does not find the file you specify, it
> > > > looks for the default file name, which is topol.tpr. That's also not
> > > > there, so you get a fatal error.
> > > >
> > > > > Here is the only thing I can susbect, but I don't know if this is
> the
> > > > > cause, but also I'm still wondering why: So When I generated my
> > ssytem
> > > > > topology using pdb2gmx
> > > > >
> > > > >
> > > > > "Now there are 3969 atoms and 124 residues
> > > > > Total mass in system 37825.764 a.m.u.
> > > > > Total charge in system -118.000 e"
> > > > >
> > > > > But when I start the solvation, the total charge of the system
> > changes
> > > > > and is no more an intger:
> > > > >
> > > > > "NOTE 2 [file topol.top, line 51]:
> > > > >    System has non-zero total charge: -117.999968
> > > > >    Total charge should normally be an integer. See
> > > > >    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > > > >    for discussion on how close it should be to an integer."
> > > > >  From the gromacs documentations, it's fine to have that slight
> > > > > non-integer charge, but I'm wondering why is that happening?!
> > > >
> > > > You have a large system with a lot of charges. You're going to
> > > > accumulate rounding error. This is not a problem.
> > > >
> > > > -Justin
> > > >
> > > > > I ran the energy minimization using these files, and it worked
> well,
> > > > > it only failing with the NVT step.
> > > > >
> > > > > I deeply aplogize for the lenghty email and for submitting the same
> > > > > email previously. The first one was not complete and was sent by
> > > > > mistake.
> > > > >
> > > > > Sincerely,
> > > > >
> > > > > Mohammed Sorour
> > > >
> > > > --
> > > > ==================================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Assistant Professor
> > > > Office: 301 Fralin Hall
> > > > Lab: 303 Engel Hall
> > > >
> > > > Virginia Tech Department of Biochemistry
> > > > 340 West Campus Dr.
> > > > Blacksburg, VA 24061
> > > >
> > > > jalemkul at vt.edu | (540) 231-3129
> > > > http://www.thelemkullab.com
> > > >
> > > > ==================================================
> > > >
> > > > --
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