Compute the MSD

LAMMPS LAMMPS Mailing List Mirror
1

Hi all,

        i am simulating a polymer system in LAMMPS . I have a single bead
particle inside my system which is interacting with other
particles via some defined interaction. Now i want to compute its
MSD. For this I am using this command

     group bead type 2
     compute 1 bead msd

Now , if I want to write the values of the msd in 'log file' by
'thermo_style', what command I have to use. I am using C_1[1]. Is it
correct ?

Thanks in advance

best,

2

Hi all,

        i am simulating a polymer system in LAMMPS . I have a single bead
particle inside my system which is interacting with other
particles via some defined interaction. Now i want to compute its
MSD. For this I am using this command

     group bead type 2
     compute 1 bead msd

Now , if I want to write the values of the msd in 'log file' by
'thermo_style', what command I have to use. I am using C_1[1]. Is it
correct ?

does it work?

axel.

3

Hi all,

        i am simulating a polymer system in LAMMPS . I have a single
bead
particle inside my system which is interacting with other
particles via some defined interaction. Now i want to compute its
MSD. For this I am using this command

     group bead type 2
     compute 1 bead msd

Now , if I want to write the values of the msd in 'log file' by
'thermo_style', what command I have to use. I am using C_1[1]. Is it
correct ?

does it work?

It definitely produces some values. But I could not get assured whether
it is the correct one which I am looking for, possibly not.

Saikat

4

Now , if I want to write the values of the msd in 'log file' by
'thermo_style', what command I have to use. I am using C_1[1]. Is it
correct ?

does it work?

It definitely produces some values. But I could not get assured whether
it is the correct one which I am looking for, possibly not.

well, nobody can confirm that from remote.
you have to be smarter about this:

pick an example that is so simple that you can compute
what you need to see manually. run only for a few MD steps
and print out the results at every step and compare what
you compute manually with what you see on the screen.
if it matches, you got it right, if it doesn't, you either used
LAMMPS wrong or did your reference calculation wrong.

axel.

5

Now , if I want to write the values of the msd in 'log file' by
'thermo_style', what command I have to use. I am using C_1[1]. Is it
correct ?

does it work?

It definitely produces some values. But I could not get assured whether
it is the correct one which I am looking for, possibly not.

well, nobody can confirm that from remote.
you have to be smarter about this:

pick an example that is so simple that you can compute
what you need to see manually. run only for a few MD steps
and print out the results at every step and compare what
you compute manually with what you see on the screen.
if it matches, you got it right, if it doesn't, you either used
LAMMPS wrong or did your reference calculation wrong.

axel.

Thanks Axel. I will try and will write back to you once I got the answer.

Saikat

6

Thanks Axel. I will try and will write back to you once I got the answer.

you are missing the point here. *don't* write back to me
(or anybody else on this list).

_you_ have to figure it out by _yourself_. it is totally
irrelevant whether i say "yay" or "nay" to what you find.
if you cannot trust yourself in figuring out and confirming
a (rather simple) procedure, you cannot do research.

the time to contact the mailing list would be in case
you encounter an inconsistency that would indicate
that there might be a bug in the LAMMPS code itself.
now, for something like an MSD computation, that is
used by a lot of people, chances of a bug are slim
(but not zero). in any case, you will have to provide
convincing evidence that something is broken and
the means to reproduce it easily.

thanks for your understanding,

     axel.