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; 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? 2) Regarding Note 1, Is it necessary to do ionization to make the system neutralize before minimization? 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. Thank you very much Best regards M.V.K
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