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<p>Hi,</p>
<p><br></p>
<p>Thanks for your suggestion. Just before we try this: the point of what I am doing is _not_ making CNT/graphene simply "run" in solvent, I know it can be done. I specifically want to reparameterize the bond, angle, and the dihedral constants with something that I know to be at least somewhat representative of graphene and isn't something from oplsaa, which comes from an entirely different paradigm. The Andrea Minoia's tutorial actually allows that level of flexibility. </p>
<p><br></p>
<p>What I understand from your suggestion is that nb parameters will be set, while all bonded parameters will be inherited from oplsaa. I am not interested in that. Can it be extended toward actually specifying the bond, angle, and dihedral energy constants, as well as their types? </p>
<p><br></p>
<p>For instance, I am comfortable with the bond type 1, angle type 2 (G96) and dihedral type #3 (Ryckaert-Bellemans), and I have exact constant values so that the experimental phonon spectrum of graphene is reproduced relatively closely. It may not matter much in a biomolecular simulation, but this level of flexibility should be available.</p>
<p><br></p>
<p>Any thoughts?</p>
<p><br></p>
<p>Thank you,</p>
<p><br></p>
<p>Alex</p>
<p><br></p>
<p><br></p>
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<p><span class=rvts7>HI, </span></p>
<p><br></p>
<p><span class=rvts7> Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines..</span></p>
<p><span class=rvts7> opls_995 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01</span></p>
<p><span class=rvts7> opls_996 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01</span></p>
<p><span class=rvts7> opls_997 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01</span></p>
<p><br></p>
<p><span class=rvts7>Here you can modify the non bonded parameters. </span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>Then in atomname2type.n2t file add the following lines.</span></p>
<p><span class=rvts7>C opls_995 0 12.011 2 C 0.142 C 0.142</span></p>
<p><span class=rvts7>C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142</span></p>
<p><span class=rvts7>C opls_997 0 12.011 1 C 0.142</span></p>
<p><br></p>
<p><span class=rvts7>Then use g_x2top. This will work.</span></p>
<p><br></p>
<p><span class=rvts7>Thanks</span></p>
<p><span class=rvts7>Abhijit</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>On Mon, Mar 23, 2015 at 8:44 AM, Alex <</span><a class=rvts8 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
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<p><span class=rvts7>Hey Justin,</span></p>
<p><br></p>
<p><span class=rvts7>Great you had a moment to look at my post.</span></p>
<p><span class=rvts7>This is an impossible task without the coordinates input file, because this is now</span></p>
<p><span class=rvts7>the realm of solid-state physics, and there really isn't a single</span></p>
<p><span class=rvts7>"residue" that can be created once and for all. It could be really</span></p>
<p><span class=rvts7>cumbersome to post everything, and sort of useless to everyone at this</span></p>
<p><span class=rvts7>point, before we figure this out.</span></p>
<p><br></p>
<p><span class=rvts7>Would you be OK with me emailing you the input along with the simple series of steps? This way you won't</span></p>
<p><span class=rvts7>need to mess with the tutorials, I'll just show you exactly what works</span></p>
<p><span class=rvts7>on my end and what doesn't.</span></p>
<p><br></p>
<p><span class=rvts7>Thanks,</span></p>
<p><br></p>
<p><span class=rvts7>Alex</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>JL> On 3/22/15 12:50 PM, Alex wrote:</span></p>
<p><span class=rvts7>>> Hi All,</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> I'm sure you've seen this many times before, but I think it might help</span></p>
<p><span class=rvts7>>> those who have never done this before, are new to Gromacs, or, like</span></p>
<p><span class=rvts7>>> me, haven't done anything relatively advanced with it in a while.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> So, here goes. My intermediate goal here was a solvated sheet of</span></p>
<p><span class=rvts7>>> graphene, so I followed </span><a class=rvts8 href="http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube">http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube</a></p>
<p><span class=rvts7>>> under "Andrea Minoia's tutorial" pretty much to the word (there is a link</span></p>
<p><span class=rvts7>>> with the exact file content). Everything prior to solvating the system</span></p>
<p><span class=rvts7>>> worked without a hitch. To solvate the system, I used genbox, making</span></p>
<p><span class=rvts7>>> it also update the topology file (created with g_x2top). This is when</span></p>
<p><span class=rvts7>>> grompp started screaming about "defaults" duplicates, and, as I tried</span></p>
<p><span class=rvts7>>> removing the #include to cnt_oplsaa.ff/forcefield.itp from the</span></p>
<p><span class=rvts7>>> topology file and just put all parameters explicitly in there, there was a bunch of other problems.</span></p>
<p><span class=rvts7>>> Without going into detail of the latter, I don't think I know what I am doing at this</span></p>
<p><span class=rvts7>>> point.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Can you please help with this task in a simple & robust step-by-step way?</span></p>
<p><span class=rvts7>>> In fact, I'd like to write up an updated tutorial</span></p>
<p><span class=rvts7>>> based on our discussion, because, among other things,</span></p>
<p><span class=rvts7>>> Andrea's parameters are taken from oplsaa on aromatics, which can and</span></p>
<p><span class=rvts7>>> should be further refined. All input is greatly appreciated and I'd</span></p>
<p><span class=rvts7>>> especially love to hear from the Gromacs superhero Justin Lemkul. :)</span></p>
<p><span class=rvts7>>></span></p>
<p><br></p>
<p><span class=rvts7>JL> At a conference, so time is limited. Provide every step of what you did and any</span></p>
<p><span class=rvts7>JL> problem you encountered. Generating the topology is the hard part; if that was</span></p>
<p><span class=rvts7>JL> generated successfully, there (in principle) shouldn't be issues. I don't do</span></p>
<p><span class=rvts7>JL> CNT simulations and don't follow those tutorials so I don't know how well they</span></p>
<p><span class=rvts7>JL> are expected to work. The .n2t file for such species should be trivial to</span></p>
<p><span class=rvts7>JL> create, and if it's derived from OPLS-AA, everything should be very straightforward.</span></p>
<p><br></p>
<p><span class=rvts7>JL> -Justin</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>--</span></p>
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<p><br></p>
<p><span class=rvts7>-- </span></p>
<p><br></p>
<p><span class=rvts7>Abhijit kayal</span></p>
<p><span class=rvts7>Research Scholar</span></p>
<p><span class=rvts7>Theoretical Chemistry</span></p>
<p><span class=rvts7>IIT Kanpur</span></p>
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<p><span class=rvts9>-- </span></p>
<p><span class=rvts9>Best regards,</span></p>
<p><span class=rvts9> Alex </span><a class=rvts10 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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