From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 10 2014 - 10:45:37 CST
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.
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