how to carry out the Coarse-Grained MD simulation Via lammps ?

Please do not send followup to individuals—send replies to the mailing list.

Force field construction and implementation is an entirely different field of endeavor than simply running simulations. You should first look to see if somebody has already studied your system and provided a force field; if not, then you need to research what people have done for similar systems and follow that (and be sure to get some assistance from someone who has actually done this before!).

—AEI

please see below for two more comments.

Please do not send followup to individuals—send replies to the mailing list.

Force field construction and implementation is an entirely different field
of endeavor than simply running simulations. You should first look to see if
somebody has already studied your system and provided a force field; if not,
then you need to research what people have done for similar systems and
follow that (and be sure to get some assistance from someone who has
actually done this before!).

—AEI

Dear Ismail,
            Thank U very much for your help. Now, the key problem I
confront is how to set the coarse-grained force field, which is wanted to
include the intermolecular Pi-Pi stacking and H-bond. Would you please give
me some advice?

a) these are questions you should discuss with your adviser. it is the
job of your adviser to advise, guide, and instruct you in your
research activities to delegate this to suitable people. a mailing
list is not able to provide this for you outside of the general
recommendations that you have received.

b) there is a bit of an inconsistency in your request. in coarse
graining you are integrating/averaging out detail to simplify your
model and thus speed up calculations to be able to handle larger
systems efficiently. both pi-pi and hydrogen bond interactions,
however, are "positional" and thus require to use a much more complex
model and that may interfere with the coarse graining goals. there
are, e.g., coarse grain DNA models out there, so it is possible, but
you have to very carefully study to what level of detail this is done
and what properties are well represented and which ones less so.

axel.