[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
Mohammed I Sorour
Mohammed.Sorour at temple.edu
Fri Aug 2 00:48:47 CEST 2019
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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