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.abra...@anu.edu.au> > Subject: Re: [gmx-users] Re: Warning and Notes in Grompp for > minimization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e50b493.3050...@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" <jalem...@vt.edu <mailto:jalem...@vt.edu>> > > Subject: Re: [gmx-users] Warning and Notes in Grompp for minimization > > To: Discussion list for GROMACS users <gmx-users@gromacs.org > > <mailto:gmx-users@gromacs.org>> > > Message-ID: <4e502903.6010...@vt.edu <mailto:4e502903.6010...@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@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 > ****************************************** >
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