Dear gmx-users<div>Good day to you<br><div>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.</div>
<div>The content of my mdp file is as below;</div><div><br></div><div><div>define = -DFLEXIBLE</div><div>constraints = none</div><div>integrator = steep</div><div>dt = 0.002 ; ps !</div>
<div>nsteps = 400</div><div>nstlist = 10</div><div>ns_type = grid</div><div>rlist = 1</div><div>coulombtype = PME</div><div>rcoulomb = 1</div><div>
vdwtype = cut-off</div><div>rvdw = 1.4 </div><div>optimize_fft = yes</div><div>;</div><div>; Energy minimizing stuff</div><div>;</div><div>emtol = 1000.0</div><div>
emstep = 0.01</div></div><div><br></div><div>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;</div>
<div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 102);">WARNING 1 [file ffbonded.itp, line 2705]:</span></div><div> Overriding Bond parameters.</div><div><br></div><div> old: 0.151 292880 0.151 292880 </div>
<div> new: C C 1 0.14210 478900</div><div><br></div><div>Generated 347361 of the 347361 non-bonded parameter combinations</div><div>Generating 1-4 interactions: fudge = 0.5</div><div>Generated 347361 of the 347361 1-4 parameter combinations</div>
<div>Excluding 3 bonded neighbours molecule type 'ICE'</div><div><br></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">NOTE 1 [file SWCNT-DDP2.top, line 15383]:</span></div><div>
System has non-zero total charge: -3.097796e-01</div><div> </div><div><br></div><div><br></div><div>Analysing residue names:</div><div>There are: 2 Other residues</div><div>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...</div>
<div>Number of degrees of freedom in T-Coupling group rest is 4371.00</div><div>Calculating fourier grid dimensions for X Y Z</div><div>Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118</div><div>Estimate for the relative computational load of the PME mesh part: 0.97</div>
<div><br></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 0);">NOTE 2 [file mdmin1.mdp]:</span></div><div> The optimal PME mesh load for parallel simulations is below 0.5</div><div> and for highly parallel simulations between 0.25 and 0.33,</div>
<div> for higher performance, increase the cut-off and the PME grid spacing</div><div><br></div><div>This run will generate roughly 0 Mb of data.</div></div><div><br></div><div>My questions:</div><div>1) May I know whether warning 1 should be taken serious?If yes, Then how to solve it?</div>
<div>2) Regarding Note 1, Is it necessary to do ionization to make the system neutralize before minimization? </div><div>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.</div>
<div><br></div><div>Thank you very much</div><div>Best regards</div><div>M.V.K</div><div><br></div><div><br></div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div><br></div></div>