Thanks for the reply. As I am new to GROMACS I am not able to understand. I will go through the manual and will get back if I have further questions.
On Tue, Feb 28, 2012 at 6:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > kirtana S wrote: > >> Thanks for the documentation. Again I have a ligand terminated silica >> nanoparticle ,what can be the easiest way to approach the topology file >> for this. >> >> >> > I don't know what the structure is, but I'll assume the .rtp route is > probably easier than writing a (presumably) repetitive topology for a > relatively large particle. You may or may not need to invoke specbond.dat > for cross-links, as pdb2gmx can deal only with linear species via .rtp > entries; other bonds are introduced with specbond.dat. > > -Justin > > >> On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> kirtana S wrote: >> >> For example if I have a polystyrene polymer chains and monomers >> of user defined solvent . I need to construct the .itp file by >> hand . >> >> >> Polystyrene is most easily generated using .rtp entries in pdb2gmx. >> The solvent can be described by manually created .itp files. >> >> >> http://www.gromacs.org/__**Documentation/How-tos/Polymers<http://www.gromacs.org/__Documentation/How-tos/Polymers> >> >> <http://www.gromacs.org/**Documentation/How-tos/Polymers<http://www.gromacs.org/Documentation/How-tos/Polymers> >> **> >> >> >> -Justin >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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