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

[Chandan Choudhury]

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 <
kmvinoth at 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.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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