Dear Justin, I am trying to use it for graphene oxide (layer), then what would be a better way if not g_x2top.
Thanks, <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=rakesh.p...@students.iiserpune.ac.in&idSignature=22> On Sun, Nov 26, 2017 at 1:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/25/17 3:12 PM, Rakesh Pant wrote: > >> Dear All, >> >> How does the utility g_x2top works? >> If we have similar connectivity in a molecule, then how will it read >> different atom types. Suppose a C atom is connected to 4 bonds (3 carbon >> atoms and 1 O atom, say in epoxy group) and similarly another C atom is >> also connected to 4 atoms (3 C atoms and 1 O atom, but the different >> functional group, e.g phenolic group). Both are present in the same >> molecule, then how should we define both in the .n2t file so that g_x2top >> reads both the atomtypes. >> > > The only difference in that case might be bond lengths, though they may > not be different enough to be distinguished (they would have to differ by > at least 10% to be outside of the default tolerance). x2top is not a > particularly smart program, and whatever it matches first will be what it > writes to the topology. If you have some very complex molecule, this may > not be a useful tool. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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 gmx-users-requ...@gromacs.org. > -- Rakesh Pant/राकेश पंत Research Fellow/अनुसंधान फेलो Indian Institute of Science Education and Research (IISER) भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान Pune-411008, India/ पुणे - ४११००८, भारत Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm -- 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 gmx-users-requ...@gromacs.org.
