HI, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01 opls_996 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01 opls_997 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01
Here you can modify the non bonded parameters. Then in atomname2type.n2t file add the following lines. C opls_995 0 12.011 2 C 0.142 C 0.142 C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 C opls_997 0 12.011 1 C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Mon, Mar 23, 2015 at 8:44 AM, Alex <[email protected]> wrote: > Hey Justin, > > Great you had a moment to look at my post. > This is an impossible task without the coordinates input file, because > this is now > the realm of solid-state physics, and there really isn't a single > "residue" that can be created once and for all. It could be really > cumbersome to post everything, and sort of useless to everyone at this > point, before we figure this out. > > Would you be OK with me emailing you the input along with the simple > series of steps? This way you won't > need to mess with the tutorials, I'll just show you exactly what works > on my end and what doesn't. > > Thanks, > > Alex > > > > JL> On 3/22/15 12:50 PM, Alex wrote: > >> Hi All, > >> > >> I'm sure you've seen this many times before, but I think it might help > >> those who have never done this before, are new to Gromacs, or, like > >> me, haven't done anything relatively advanced with it in a while. > >> > >> So, here goes. My intermediate goal here was a solvated sheet of > >> graphene, so I followed > http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube > >> under "Andrea Minoia's tutorial" pretty much to the word (there is a > link > >> with the exact file content). Everything prior to solvating the system > >> worked without a hitch. To solvate the system, I used genbox, making > >> it also update the topology file (created with g_x2top). This is when > >> grompp started screaming about "defaults" duplicates, and, as I tried > >> removing the #include to cnt_oplsaa.ff/forcefield.itp from the > >> topology file and just put all parameters explicitly in there, there > was a bunch of other problems. > >> Without going into detail of the latter, I don't think I know what I am > doing at this > >> point. > >> > >> Can you please help with this task in a simple & robust step-by-step > way? > >> In fact, I'd like to write up an updated tutorial > >> based on our discussion, because, among other things, > >> Andrea's parameters are taken from oplsaa on aromatics, which can and > >> should be further refined. All input is greatly appreciated and I'd > >> especially love to hear from the Gromacs superhero Justin Lemkul. :) > >> > > JL> At a conference, so time is limited. Provide every step of what you > did and any > JL> problem you encountered. Generating the topology is the hard part; if > that was > JL> generated successfully, there (in principle) shouldn't be issues. I > don't do > JL> CNT simulations and don't follow those tutorials so I don't know how > well they > JL> are expected to work. The .n2t file for such species should be > trivial to > JL> create, and if it's derived from OPLS-AA, everything should be very > straightforward. > > JL> -Justin > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
