[gmx-users] Re: Warning and Notes in Grompp for minimization
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Aug 21 09:32:35 CEST 2011
On 21/08/2011 4:42 PM, meisam valizadeh kiamahalleh wrote:
> 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?
Each molecule has to have an integer for its total charge. You'll need
to investigate in your .top file why this is not the case.
> >>May I know whether my mdp file contents (rlis, rcoulomb,vdwtype
> and rvdw) are correct?
They're not evidently wrong, but you need to choose these kinds of
parameters to be consistent with the force field you are using. If
someone's parametrized cis-platin with a carbon nanotube, then you have
simply to copy what they did. If not, then you are very likely to
struggle to get something working that proves to be a valid model - and
very much more so if this happens to be your first excursion into MD
simulations. See
http://www.gromacs.org/Documentation/How-tos/Parameterization
Mark
> 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 <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4E502903.6010100 at vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
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