[gmx-users] Reg: Putting molecules on one side of the box

[Mark Abraham]

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 <kmvinoth at 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 at 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.abraham at 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 <kmvinoth at 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 at 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 at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
> --
>  gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
 > -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101004/1204925c/attachment.html>