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http://archive.ambermd.org/201411/0162.html
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HTH,
Jason
On Mon, 2014-11-17 at 23:00 +0530, Robin Jain wrote:
> My question is that my box is cubic and i want to maintain periodic
> boundary condition also then am i going in right way or not.
>
> On Thu, Nov 13, 2014 at 11:29 AM, Robin Jain <robinjain.chem.gmail.com>
> wrote:
>
> >
> > Dear all,
> > I want to simulate an organic molecule in methanol. Since i want to
> > simulate it in fix no. of methanol 80 and box size 17.58. For this i have
> > follow this process-
> >
> > first i used *AddtoBox* command to simulte my sytem with fix no. of
> > solvent and then i go to *xleap* and used *setbox* command and then i
> > used *saveamberparm* command for *prmtop* and *inpcrd* file and finally i
> > used *chbox* command to get desired box dimension in inpcrd file and then
> > i manually edit prmtop file in FLAG_BOX_DIMENSIONS.
> >
> > Now i want to know that have i done right or wrong and how could i manage
> > periodic boundary condition in that.
> > --
> > Robin Jain
> >
> >
> >
>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 17 2014 - 11:00:02 PST
