Manual section 4.2.13 maybe not enough. My potential functional shape is much more complex. I need at least two different force constants as C6 and C12 in LJ potential function in section 6.7.2. I use this for block copolymer system. There is only two types of monomer(e.g. A, B) and two types of bond potential(e.g.A-A, B-B ). If I can form two tables related to the two different bond potential respectively (e.g. table 1 for A-A and table 2 for B-B), the problem will be solved. Is it possible to be done in Gromacs?
On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jia Haitao wrote: > >> Hello, everyone >> >> In gromacs user manual 6.7, they form non-bond potentials using table >> files, What should I do if I want to use a new *Bond* potential? The new >> bond potential combines two harmonic bond potentials, >> Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a standard harmonic >> potential. >> Besides, according user manual 5.7, there is 10 function types in table >> 5.5. How can I use the 8th and 9th type? Is there some examples? . >> > > All the information related to what you want to do is in the manual, > section 4.2.13. Per the caption of Table 5.5, bond type 8 will be used to > generate exclusions (when running grompp); presumably type 9 will not. > Hopefully someone will correct me if I'm wrong here. > > -Justin > > -- >> */ >> >> Jia Haitao >> State Key Laboratory of Polymer Physics and Chemistry >> Changchun Institute of Applied Chemistry >> Chinese Academy of Sciences >> Changchun 130022, CHINA >> /* >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- * Jia Haitao State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022, CHINA *
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