Hello Anne,
Your questions seem to be very confusing. If you would like to study your
system in gas phase, you probably don't need a periodic box because that is
used for explicit solvent conditions. You cannot force your small molecule
to move towards the bigger one by keeping some of your atoms "at the
same coordinates", because that is not a correct way to study dynamics. My
suggestion is that you might need a better understanding and description of
your project, and then consider what the best way/tool is to achieve your
goals.
Best,
Jane
On Thu, Feb 7, 2013 at 2:54 AM, Anne Kichler <a_kichler.ymail.com> wrote:
> Hello Amber users,
>
> This is my first time, whenI do MD. So, my questions could seem so basic.
>
> I have system ( two molecules ) in gas phase in periodic box. I want add
> pseudo-atom inside the big one molecule, which contains 150 atoms. Then put
> the considers between pseudo-atom and small molecule, 39 atoms.
> Additionally, I want determine, that four atoms of big molecules will be
> during the simulations at the same coordinates (don't move)-it's necessary,
> because my idea is observe how the small molecules go inside to the big
> particle.
>
> Now, I have questions:
> -when I must add pseudo-atom? during parametrizing in xleap? -what command?
> - how can I cause the atoms in big molecule be in this same place during
> MD? (Do I must write script orin files add notes?)
>
> Thank you in advance,
> Anne Kichler
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 08 2013 - 14:00:02 PST
