Re: namdplot

From: vivek sharma (vivek.sharma_at_helsinki.fi)
Date: Thu Dec 09 2004 - 10:38:14 CST

Hello everybody,

Thanks for the help.
So this means a run (constant temperature/presuure options 'off' +
boundary conditions 'on')will give NVE ensemble simulation and a run
(constant pressure option 'off' + constant temperature option 'on' +
boundasry condition 'on') will give NVT ensemble simulations.

But out of curiosity I ask , if I keep boundary conditions 'off' or say do
not use them in the above mentioned two cases , then such ensembles will
be of type NE (N and E constant) and NT (N and T constant), respectively.
But theoretically, such ensemble does not exist. Statistical Mechanics
uses the concept of volume of system in picturising the ensemble (all
replicas of system are confined in some volumes), then is it right to run
such 'NE' / 'NT' type of simulation? Ofcourse then the system to be
simulated will lie in infinite vacuum.

Thanking you once again,

sincerely,

Vivek Sharma

Quoting nordgren_at_sas.upenn.edu:

> Hi Vivek,
>
> I can't really comment on your first question, since I have no
> experience
> with NAMDplot. But as for constant-volume dynamics, well, basically
> that's
> what you get unless you specifically use constant pressure. In other
> words,
> if you don't invoke one of the NAMD options to use constant pressure,
> then
> the size of your MD box will remain static, i.e., constant volume.
>
> Of course, the concept of a "box" and a "volume" only make sense if you
> are
> using some sort of periodic boundary conditions for your system...
> otherwise,
> you have a cluster of atoms surrounded by infinite vacuum....
>
> So, just use one of the constant-temperature methods, along with
> periodic
> boundaries (but without constant pressure) and you have NVT dynamics.
>
> good luck,
> Erik
>
>
> C. Erik Nordgren, Ph.D.
> Department of Chemistry
> University of Pennsylvania
>
>
> Quoting vivek sharma <vivek.sharma_at_helsinki.fi>:
> > 2. Also I want to know is there a way to run NVT ensemble in NAMD, I
> see
> > the
> > methods and options for constant Temperature and constant Pressure,
> but
> > not
> > for constant volume. Please explain briefly.
> >
> > Thanking you,
> >
> > sincerely
> >
> > Vivek (NAMD newbie)
>
>

```--
VIVEK SHARMA
HBG BI
```

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