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

[vinothkumar mohanakrishnan]

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.abraham at 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 <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
>> > > --
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