Re: How to run NVT simulations without applying periodic boundary conditions?

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Wed Feb 20 2008 - 13:59:44 CST

Harish-

Thanks for reminding me of the simulations with spherical boundary
conditions.

The ideal solution I want is to have a box for the NVT simulation, instead
of a sphere. But yeah, I will see how the water sphere works out for my
problem.

Thanks,
Long

On Feb 20, 2008 2:10 PM, harish vashisth <harish.vashisth_at_gmail.com> wrote:

> yes. I think you can use instead spherical boundary conditions. Solvate
> your protein in water sphere. Tutorial has all details on how to do such
> stuff in routine.
>
> -Harish
>
>
> On Wed, Feb 20, 2008 at 1:16 PM, Yinglong Miao <yimiao_at_indiana.edu> wrote:
>
> > Dear NAMD developers/users,
> >
> > It has been discussed about running NVT simulations with applying
> > periodic boundary conditions (PBC). But can anyone tell me whether NAMD
> > provides the option to run NVT simulations without applying PBC (i.e.,
> > the system in a SINGLE constant closed volume)? I think it's much easier to
> > implement, but I haven't found any related simulations. If the option is
> > provided, how to set the configuration parameters for the simulations?
> >
> > Thanks,
> > Long
> >
> > --
> > Yinglong Miao
> > Ph.D. Candidate
> > Center for Cell and Virus Theory
> > Chemistry Department, Indiana University
> > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > Tel: 1-812-856-0981
>
>
>

-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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