[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

Fri Aug 2 00:40:33 CEST 2019

>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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