Dear, Alex Does it mean, we do not need to define all the atomtypes in the .nt2 file. It is enough to define all types in bonded and non-bonded itp.
Thanks, Rakesh <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 3:27 PM, Alexandr Nasedkin <nased...@chalmers.se> wrote: > Edit the content of you ffnonbonded.itp file approximately this way: > > [ atomtypes ] > ;name at.num mass charge ptype sigma epsilon > C 14 12.00 1.08 A 0.44000 0.63 ; > OCE 8 15.999400 -0.70 A 0.35400 0.159705 ; C-O-C > Bridging Oxygen; > OCH 8 15.999400 -0.51 A 0.35400 0.159705 ; C-O-H > Oxygen; > > HCO 1 1.008000 0.32 A 0.04490 0.235725 ; H-O-C > Hydrogen; > .... > > You would need to search literature for respective ff parameters: all the > above parameters are taken from another topology to give a template. > > > -Alex > > > On 26/11/2017 10:37, Rakesh Pant wrote: > >> Dear Alex, >> If I use O atoms to define the respective functional groups, then how to >> include the C atoms present in the molecule. >> >> Thanks, >> Rakesh >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io/install?source=signature&lang=en&refer >> ral=rakesh.p...@students.iiserpune.ac.in&idSignature=22> >> >> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nased...@chalmers.se> >> wrote: >> >> Hi, >>> >>> As I understood the problem, you need to distinguish between surface and >>> buried carbons? >>> >>> You could define two atomtypes that differ in name and use it to process >>> with x2top. >>> >>> Below is an example of *.n2t lines. You would need to change the charges >>> and bondlengthes. >>> >>> ... >>> >>> O OCH -1.05 15.9994 2 C 0.154 H 0.1 ; oxygen, -OH >>> group >>> O OCE -1.05 15.9994 2 C 0.154 C 0.154 ; bridge >>> oxygen >>> >>> ... >>> >>> Then you need *.n2t file in your ff. >>> >>> Good luck! >>> >>> >>> -Alex >>> >>> >>> On 25/11/2017 22:06, Justin Lemkul wrote: >>> >>> >>>> On 11/25/17 3:31 PM, Rakesh Pant wrote: >>>> >>>> But then I how will include the C atom (which is also one of the >>>>> atomtypes)? >>>>> >>>>> No idea, but I know people on this list have dealt with graphene oxide >>>> before, so hopefully someone else chimes in. >>>> >>>> -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 gmx-users-requ...@gromacs.org. >>> >>> >> >> > -- > 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.
