[gmx-users] gmx-users Digest, Vol 88, Issue 131
meisam valizadeh kiamahalleh
meisam488 at gmail.com
Mon Aug 22 08:50:59 CEST 2011
Dear Mark
Thank you very much for your kind reply and advice.
Actually I have the parameters for cisplatin and carbon nanotubes. and I
have generated all forcefield parameter properly. there is no mis-matching.
I have solved the non-integer charge problem by modifying the topology file
manually as far as I had the charges value from literature.
But I still have one note which stop the calculation of minimization. The
note is as stated below. Kindly would you please help me on how to solve
this matter?
NOTE 1 [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
Thank you very much
Meisam
Message: 1
> Date: Sun, 21 Aug 2011 17:32:35 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Warning and Notes in Grompp for
> minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E50B493.3050508 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
> >
> > ========================================
> >
> >
> >
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110821/6ce19dcb/attachment-0001.html
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 88, Issue 131
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110822/c8221470/attachment.html>
More information about the gromacs.org_gmx-users
mailing list