Hi Vinoth !! Try genbox with increasing the vander Waal's radii.
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Oct 4, 2010 at 5:03 PM, vinothkumar mohanakrishnan < kmvin...@gmail.com> wrote: > > 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 >
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