[gmx-users] Warning and Notes in Grompp for minimization

[Justin A. Lemkul]

meisam valizadeh kiamahalleh wrote:
> Dear gmx-users
> Good day to you
> I have a system including carbon nanotube (1260atoms) and 18 Cisplatin 
> molecules (198atoms) =1458atoms. I have created the topology file of the 
> system and now I would like to run minimization on this system.
> The content of my mdp file is as below;
> 
> define               = -DFLEXIBLE
> constraints          = none
> integrator           = steep
> dt                   = 0.002     ; ps !
> nsteps               = 400
> nstlist              = 10
> ns_type              = grid
> rlist                = 1
> coulombtype          = PME
> rcoulomb             = 1
> vdwtype              = cut-off
> rvdw                 = 1.4  
> optimize_fft         = yes
> ;
> ;        Energy minimizing stuff
> ;
> emtol                = 1000.0
> emstep               = 0.01
> 
> After entering the command; grompp -f mdmin1.mdp -c SWCNT-DDP-box.pdb -p 
> SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 , However a wrong TPR file 
> is generated, I also get 2 notes and 1 warning as stated below;

The -maxwarn option should almost never be used.  If you're overriding warnings 
that grompp is producing, they typically only occur if the system will become 
unstable.  Beware.

> WARNING 1 [file ffbonded.itp, line 2705]:
>   Overriding Bond parameters.
> 
>   old: 0.151 292880 0.151 292880 
>   new: C        C        1     0.14210   478900
> 
> Generated 347361 of the 347361 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 347361 of the 347361 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'ICE'
> 
> NOTE 1 [file SWCNT-DDP2.top, line 15383]:
>   System has non-zero total charge: -3.097796e-01
>   
> 
> 
> Analysing residue names:
> There are:     2      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting 
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 4371.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118
> Estimate for the relative computational load of the PME mesh part: 0.97
> 
> NOTE 2 [file mdmin1.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
> 
> This run will generate roughly 0 Mb of data.
> 
> My questions:
> 1) May I know whether warning 1 should be taken serious?If yes, Then how 
> to solve it?

You have different bonded parameters assigned for a single bond type.  You 
should investigate why you've produced different parameters for the same 
interaction and correct it, if necessary.  If you are trying to override 
existing parameters, this may be what you want.  Otherwise, eliminate the 
duplicate entry such that the parameters you actually wish to use are being 
assigned.

> 2) Regarding Note 1, Is it necessary to do ionization to make the system 
> neutralize before minimization? 

Not in this case.  You have a non-integer charge of sufficiently disturbing 
magnitude (i.e., it does not arise simply due to floating point arithmetic), 
indicating that the charges assigned in the topology are junk.

> 3) Regarding Note 2, Is there anything wrong with my mdp file or it is 
> because of using a computer with small processor. Actually I just tried 
> to do this minimization on my laptop for the first time. If the 
> processor is too small for this calculation, I may be able to work with 
> our cluster if it is advised.

For minimization, this often happens.  It is unimportant in this case.

-Justin

> 
> Thank you very much
> Best regards
> M.V.K
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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