[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 00:29:41 CEST 2019

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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