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 > 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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