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

[meisam valizadeh kiamahalleh]

Dear Justin
Thank you very much for your reply
>>Regarding Warning 1; Yes, I have introduced the new parameter for C C bond
and it is what I want.
>>Regarding Note 1;  Actually, the charges for each atom in topology file
are what I included myself in Cisplatin parameters based on the literature.
May I know what should I do if I have non-integer charge in this case?
>>May I know whether my mdp file contents (rlis, rcoulomb,vdwtype and rvdw)
are correct?
Thanks so much
M.V.K



> Message: 3
> Date: Sat, 20 Aug 2011 17:37:07 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Warning and Notes in Grompp for minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E502903.6010100 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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
> >
> >
> >
>
> --
> ========================================
>
> 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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