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

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Thu Feb 21 2008 - 08:24:55 CST

For NVT simulations with PBC, molecules are wrapped from one side to the
other side to avoid evaporation. I am doing some calculations with the
atomic coordinates and the wrapping of molecules will mess up my
calculations. So I want to keep all molecules in the volume without
wrapping. Yeah, I will try applying boundary constraints and/or the constant
spherical volume as Jeff and you suggested.

Thanks,
Long

On Thu, Feb 21, 2008 at 3:10 AM, Leandro Martínez <
leandromartinez98_at_gmail.com> wrote:

> Ah, ok, so you need to add some kind of restraint to avoid you molecules
> to leave the volume you want (why would you want that?). You can do
> in namd I think. Without adding restraints it is not possible to do what
> you want.
> Leandro.
>
>
>
>
>
> On Wed, Feb 20, 2008 at 10:55 PM, Yinglong Miao <yimiao_at_indiana.edu>
> wrote:
>
> > But you need to set the three cellbasisvectors for constant volume. That
> > indicates PBC. So I'm saying the NVT ensemble option for a single closed box
> > with constant volume may be missed in NAMD.
> >
> > Thanks,
> > Long
> >
> > On Wed, Feb 20, 2008 at 3:53 PM, Leandro Martínez <
> > leandromartinez98_at_gmail.com> wrote:
> >
> > >
> > > Just set the three axis and do NOT set constant pressure coupling.
> > > That will give
> > > a NVE simulation. If you put some temperature scaling you get your
> > > NVT simulation.
> > > If you don´t put neither the axis nor pressure coupling, you get a
> > > simulation without
> > > any periodic boundary condition.
> > > Leandro.
> > >
> > >
> > >
> > > On Wed, Feb 20, 2008 at 7:16 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
>
>
>

-- 
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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