radial distribution function

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1

Dear LAMMPS users ,

Greetings .

I want to calculate radial distribution function from the center of mass for fullerene ( C60 ) .

Is it possible with LAMMPS ?
Can I use " compute com " command ?
http://lammps.sandia.gov/doc/compute_com.html

Thanks for your attention .

Regards,
Saeed .

2

I forgot to say that I have fullerene inside of water molecules and I want to calculate RDF from center of mass of fullerene to oxygen atom of water molecules .

3

Dear LAMMPS users ,

Greetings .

I want to calculate radial distribution function from the center of mass for fullerene ( C60 ) .

Is it possible with LAMMPS ?
Can I use " compute com " command ?
http://lammps.sandia.gov/doc/compute_com.html

No

4

2015-04-01 11:49 GMT+02:00 SaeeD PourasaD <[email protected]...>:

I forgot to say that I have fullerene inside of water molecules and I want
to calculate RDF from center of mass of fullerene to oxygen atom of water
molecules .

Dear LAMMPS users ,

Greetings .

I want to calculate radial distribution function from the center of mass
for fullerene ( C60 ) .

There's the compute rdf command, but it only calculated the "real" rdf
between all pairs in the specified groups. I think you're best off by
either writing your own compute (based on the existing compute rdf), our do
it in post-processing of dump files.

Kristof

5

saaed,

you are running the C60 as rigid objects, yes?
then you could add an atom with a tiny mass (say 1.0e-10) with zero
potential energy in the center of each C60 and then compute the g(r)
relative to this reference particle. otherwise you need to post
process.

axel.

6

Hi .
Greetings.
Thanks alot for you replay.
I have no idea about post-processing so i will check it .

About Axel’s suggestion , that is very nice idea i will do that ^^

Regards,
Saeed.

7

A conceptual note. The comptue rdf command

calculates an RDF between pairs of atoms.

There is no command in LAMMPS to compute

RDFs between arbitrary point(s) and atoms.

I suppose one could be written to infer points

from the COM or geometric center of a molecule

and compute an RDF between those points and

all other atoms. The new compute com/chunk

would be a starting point, since it shows how

to calculate the COM of each chunk and chunks

can be molecules.

So a new compute rdf/chunk would be possible.

Steve

8

Hi .
Dear LAMMPS users ,
I have a C60 inside of plenty of water molecules.
I want to calculate COM radial distribution function. I used Axel’s suggestion ;I add an atom with a tiny mass (say 1.0e-10) with zero
potential energy in the center of C60 .
Unfortunately the result is not OK , and I get large amount for RDF .

Do you have any suggestion for solving this problem ?

a part of my data file :
4 atom types

3 bond types
3 angle types
1 dihedral types
1 improper types

-50.0 40 xlo xhi
-50.0 40 ylo yhi
-50.0 40 zlo zhi

Masses

1 12.011 #CA “Aromatic C” 6 partial charge=-0.115
2 15.9994
3 1.008
4 1.0e-10 #this is inside of C60 for COM_RDF !

and a part of my input file :

…
group C60_COM type 1 4

…
NVT

fix 1 SPC shake 1.0e-4 500 1000 a 2 b 2

fix 2 SPC nvt temp 298.0 298.0 100.0

fix 4 C60_COM rigid/nvt molecule temp 298.0 298.0 100.0
time step 0.05

run 2000000

…

NPT

fix 5 SPC npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 dilate all

fix 6 C60_COM rigid/nvt molecule temp 300.0 300.0 100.0

compute myRDF all rdf 250 4 3
fix 7 all ave/time 2 500 5000 c_myRDF file COM.rdf mode vector

time step 1.0
run 1000000

Thanks in advance .

Best ,
Saeed.

9

Dear Axel ,

Do you have any idea about this ? I can not understand the reason of this result .