Re: Re: Periodic Boundary conditions

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 02 2011 - 06:19:54 CDT

On Thu, Jun 2, 2011 at 4:14 AM, <ishiikai08_at_yahoo.co.jp> wrote:
> Dear Jim
>
> Thank you for your reply.
>
> I have a question.
>
> Can I make the cell dimensions into time-variable value?
>
> In other words, for example, is it possible that the cellBasisVector
> increases as time passes?

to the best of my knowledge, no. not with namd.
there are other MD codes, however, that allow you
to have a programmed simulation cell deformation.

it always helps in cases like this, if you explain a little
bit what you are trying to learn from this procedure and
what you system is going to be that you are planning
to simulate.

cheers,
    axel.

axel.
>
> If this is a poor question, I'm sorry.
>
> Ishii Kai, Japan
>
>                        >
>>  Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> A constant pressure method such as Langevin piston will allow the cell
> dimensions to vary.  PME is compatible with constant pressure methods.
>
> -Jim
>
> On Wed, 1 Jun 2011, ishiikai08_at_yahoo.co.jp wrote:
>
>> Hi, NAMD Users.
>
> I read the tutorial, the user's guide and archive.
>
> But I could not find the way to change the cellBasisVector
> of Periodic Boundary conditions into variable number.
> That is, I hope that the cellBasisVector is not constant value but
> time-variable value.
>
> Please tell me the way to change that.
> Then similarly, I hope that PME is time-variable value.
>
> If this is a poor question, I'm sorry.
> I'm beginner of NAMD and English.
>
> Thanks.
> Ishii Kai
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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