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" <[email protected]> > Subject: Re: [gmx-users] Warning and Notes in Grompp for minimization > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > > ======================================== > >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
