hi Mark After deleting half the molecules of decane from the box and if i use genbox to add water then i will only get a mixture where as i want an interface to be formed.that will be more useful to me.
Regards Vinoth On Mon, Oct 4, 2010 at 4:44 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > Yes, giving you a set of commands would be the simplest thing for you :-) > However I can't give you a set of commands for an arbitrary such operation, > because there's a whole set of conditions you haven't stated. Moreover, > figuring out the fine detail would take time that I don't have available. > Finally, you wouldn't learn how to do solve such problems for yourself, and > would remain dependent, instead of developing a set of skills that is useful > for your work :-) > > Be sure to read the documentation for each of the tools I have mentioned, > and please do ask a focussed question on the list if you run into problems. > > Good luck! > > > Mark > > ----- Original Message ----- > From: vinothkumar mohanakrishnan <kmvin...@gmail.com> > Date: Monday, October 4, 2010 21:58 > Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > can you tell this with the help of the command.... that will be more > useful > > > > Regards > > Vinoth > > > > On Fri, Sep 24, 2010 at 12:58 PM, Mark Abraham > > <mark.abra...@anu.edu.au>wrote: > >> > Use genconf to replicate some suitable smaller box of decane to the >> full size, delete the second half of the decane molecules, then use genbox >> to fill the rest with water. Cunning use of genconf should allow you to >> select where the division lies. >> > >> > Mark >> > >> > >> > ----- Original Message ----- >> > From: vinothkumar mohanakrishnan <kmvin...@gmail.com> >> > Date: Friday, September 24, 2010 17:22 >> > Subject: [gmx-users] Reg: Putting molecules on one side of the box >> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> > >> > > Hi all >> > > >> > > I have a triclinic box of length of 8*3*3 nm. i want to put water on >> one side of the box and say decane on the other side of the box. How to >> generate .gro for the water-decane mixture such that they form two distinct >> parts of the box. >> > > >> > > Regards >> > > Vinoth >> > > -- >> > > 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 >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > 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 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 >> > > > > -- > > 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 > > -- > 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 >
-- 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
