Re: Volume Entry

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 10 2014 - 11:09:18 CST

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.

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