From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Sun Feb 16 2014 - 10:29:18 CST
Dr. Axel,
I got the C4F10 experimental density, then I built the box volume based on
that value. unfortunately, I got the message " the cell is too small"
On Mon, Feb 10, 2014 at 12:09 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Feb 10, 2014 at 12:04 PM, Rawan Al Nsour <alnsourra_at_vcu.edu>
> wrote:
> > First, many thanks for you sir for taking the time to reply.
> > what I want to do is to find the density for small fluorocarbons such as
> > c6f14, but it is very small molecule
>
> so what?
>
> please read my answer again, think about it for a bit and hopefully
> you'll figure out where you are going in the wrong direction.
>
> axel.
>
> > On Mon, Feb 10, 2014 at 11:45 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> please always copy the mailing list on your responses, so the
> >> discussion gets properly archived and people can later look up the
> >> outcome (and save time by not having to ask the same question).
> >>
> >> On Mon, Feb 10, 2014 at 11:25 AM, Rawan Al Nsour <alnsourra_at_vcu.edu>
> >> wrote:
> >> > Do you mean they are Zero
> >>
> >> or at best ill-defined.
> >>
> >> > then how can I find c6f14 density
> >>
> >> now *that* is a different question. density is computed from the total
> >> mass in a reference volume. while it may be difficult to define the
> >> reference volume for a single molecule, it is rather straightforward
> >> to do so for a bulk system, provided you have a homogeneous
> >> distribution of the density (at least at the scale and level of
> >> accuracy that you are looking at). if you do not have a bulk system,
> >> like in the case you are describing, you have to determine a suitable
> >> reference volume yourself (e.g. through 3d-binning) and can try to
> >> compute the density for this/these references through averaging.
> >>
> >> in short, you have to properly define what you are computing, because
> >> what you are asking for is not well defined.
> >>
> >> axel.
> >>
> >>
> >>
> >> > On Mon, Feb 10, 2014 at 11:12 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> > wrote:
> >> >>
> >> >> On Mon, Feb 10, 2014 at 11:08 AM, Rawan Al Nsour <alnsourra_at_vcu.edu>
> >> >> wrote:
> >> >> > I simulated a small molecule c6f14 without (PBC's and PME), I did
> not
> >> >> > see
> >> >> > the volume entry in the output file, how can I measure the volume?
> >> >>
> >> >> counter question: what is the volume of a point particle?
> >> >>
> >> >> bonus question: what is the volume of a collection of point
> particles?
> >> >>
> >> >> axel.
> >> >>
> >> >> > Thanks
> >> >> >
> >> >> > --
> >> >> > Rawan Al Nsour
> >> >> > Ph.D. Candidate
> >> >> > Department of Mechanical and Nuclear Engineering
> >> >> > School of Engineering, Virginia Commonwealth University
> >> >> > E-mail: alnsourra_at_vcu.edu
> >> >> > 401 W. Main Street, Room E3216
> >> >> > P.O. Box 843015
> >> >> > Richmond, Virginia 23284-3015
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> College of Science & Technology, Temple University, Philadelphia PA,
> >> >> USA
> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Rawan Al Nsour
> >> > Ph.D. Candidate
> >> > Department of Mechanical and Nuclear Engineering
> >> > School of Engineering, Virginia Commonwealth University
> >> > E-mail: alnsourra_at_vcu.edu
> >> > 401 W. Main Street, Room E3216
> >> > P.O. Box 843015
> >> > Richmond, Virginia 23284-3015
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> >
> > --
> > Rawan Al Nsour
> > Ph.D. Candidate
> > Department of Mechanical and Nuclear Engineering
> > School of Engineering, Virginia Commonwealth University
> > E-mail: alnsourra_at_vcu.edu
> > 401 W. Main Street, Room E3216
> > P.O. Box 843015
> > Richmond, Virginia 23284-3015
> >
> >
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
-- Rawan Al Nsour Ph.D. Candidate Department of Mechanical and Nuclear Engineering School of Engineering, Virginia Commonwealth University E-mail: alnsourra_at_vcu.edu 401 W. Main Street, Room E3216 P.O. Box 843015 Richmond, Virginia 23284-3015
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