hi all
i am trying to simulate fluid flow through carbon nanotubes. i am nw hit upon a doubt and hope that u cn clear tis for me. i use harmonic style bonds for both carbon nanotube and fluid. however, wen we r specifying the bond coeff for the 2 hw can v b sure tat the coeff r being assigned to the proper bonds. in other words, how can i assign bondstyle 1 to the c-c bond and bondstyle 2 to the fluid bond.
thanking ou in advance
unni
hi all
hi,
first off, i think you should check your keyboard. there seems to be
something wrong with it. your inquiry is almost unreadable due to
a lot of letters are missing.
i am trying to simulate fluid flow through carbon nanotubes. i am nw hit
upon a doubt and hope that u cn clear tis for me. i use harmonic style bonds
for both carbon nanotube and fluid. however, wen we r specifying the bond
coeff for the 2 hw can v b sure tat the coeff r being assigned to the proper
i don't understand your question. if you define a bond in a data file, you
also have to set its bond type and that links it to the parameters for
that style.
bonds. in other words, how can i assign bondstyle 1 to the c-c bond and
bondstyle 2 to the fluid bond.
how do you define your bonds now then without specifying the style?
axel.
hi all
first of all, sorry for using shortcuts in the mail…i was a bit excited while typing the mail…
what i actually meant was…i created 2 pdb files for CNT and fluid. then combined the 2 using
topotools…then i converted it to lammps format using writelammpsdata command…but in that only bond types are specified…so my doubt is when we specify the angle coeff how do we make sure that they are for the correct molecules…i checked the manual but couldnt find the answer…in other words when we type the commands
angle_coeff 1 5.6 3.1
angle_coeff 2 5.9 4
how do we make sure that the angle type 1 is for the fluid itself…
i know its a silly doubt…it would be really helpful if somebody could clear this…
thanking you in advance
unni
hi all
first of all, sorry for using shortcuts in the mail...i was a bit excited
while typing the mail....
what i actually meant was..i created 2 pdb files for CNT and fluid. then
combined the 2 using
topotools..then i converted it to lammps format using writelammpsdata
here is your mistake. pdb files only contain coordinates. VMD will
guess bonds upon reading them based on some internal heuristics
for visualization only. it will not assign bond types, nor define angles,
dihedrals or impropers or anything like that. the topotools packages
has additional functionality to aid you with adding or modifying that
kind of information, but by default it assumes that you have already
provided that data in one way or another before writing a data file.
VMD is totally agnostic of the chemistry of what you are modeling.
in fact, if you plan to use a many-body potential to model the CNT,
you'll have to remove the automatically assigned bonds for those
atoms, as those potentials already contain contributions from bonded
interactions in the non-bonded terms.
command...but in that only bond types are specified..so my doubt is when we
specify the angle coeff how do we make sure that they are for the correct
molecules...i checked the manual but couldnt find the answer....in other
you won't find any of that in the lammps manual. lammps assumes
that you know what you are doing, when you create a data file.
words when we type the commands
angle_coeff 1 5.6 3.1
angle_coeff 2 5.9 4
how do we make sure that the angle type 1 is for the fluid itself......
you first have to define the angles that you want to assign
force field parameters to.
i know its a silly doubt....it would be really helpful if somebody could
clear this....
always remember that computers are dumb. they do _exactly_ what
you tell them to do. nothing more, nothing less. so _you_ have to make
sure that what you tell them to do, is what you want.
axel.
Dear Axel
thank you for spending your valuable time for me…
unni