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. :)
At a conference, so time is limited. Provide every step of what you did and any problem you encountered. Generating the topology is the hard part; if that was generated successfully, there (in principle) shouldn't be issues. I don't do CNT simulations and don't follow those tutorials so I don't know how well they are expected to work. The .n2t file for such species should be trivial to create, and if it's derived from OPLS-AA, everything should be very straightforward.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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].
