Coarse Grained model

Hi LAMMPS Users,

I want to implement the Coarse Grained MD with shinoda et. al model…

I got bond angle and non-bonded parameters,
Installed user-CG-CMM package and started running CGMD.

Now Can anyone help me how to choose following things while runnning CGMD in LAMMPS.

  1. angle_style harmonic and angle_style cg/cmm.

I read cg/cmm comes with harmonic potential and nonbonded parameters between 1 3 atoms.

but can’t decide myself to have simple harmonic or cg/cmm

  1. about atom_style angle or full.

angle just has to calculate bond and angles

In my system, mapping scheme reduced me to only beads with bonds and angles… then can i use atom_style angle.

Thanks in advance

Karteek kumar

Molecular simulation lab,
JNCASR

Hi LAMMPS Users,

I want to implement the Coarse Grained MD with shinoda et. al model..

I got bond angle and non-bonded parameters,
Installed user-CG-CMM package and started running CGMD.

Now Can anyone help me how to choose following things while runnning CGMD
in LAMMPS.

i can try.

1. angle_style harmonic and angle_style cg/cmm.

  I read cg/cmm comes with harmonic potential and nonbonded parameters
between 1 3 atoms.

but can't decide myself to have simple harmonic or cg/cmm

you should use neither! please use

angle_style sdk

the cg/cmm styles are only provided for backward
compatibility. the model is now officially called SDK
model and the corresponding styles are the pair styles
lj/sdk, lj/sdk/coul/long, and the angle style sdk
for lj/sdk/coul/long also using pppm/cg might be
beneficial, but is not mandatory.

2. about atom_style angle or full.

angle just has to calculate bond and angles

atom_style full is needed if your model
includes charged beads otherwise angle
will be sufficient.

In my system, mapping scheme reduced me to only beads with bonds and
angles... then can i use atom_style angle.

it has nothing to do with that, it is the charges
that matter. atom_style angle, only supports
uncharged particles.

axel.

Hi Axel sir,

For pair_style lj/sdk and angle style sdk, where can i find the documentation.

whether we need to include optional package…

Thanks in advance.

Karteek kumar

Molecular simulation lab,
JNCASR

But

Hi Axel sir,

For pair_style lj/sdk and angle style sdk, where can i find the
documentation.

whether we need to include optional package..

they are part of the USER-CG-CMM package.
the code is effectively the same, using the
cg-cmm versions of the styles will allow to read
older inputs without modifications.

all new projects should only use the sdk styles.

the backward compatibility layer will be removed
some time in the future when all system preparation
tools have been adapted or new/better once written;
whichever happens first.

cheers,
     axel.

For pair_style lj/sdk and angle style sdk, where can i find the
documentation.

doc/angle_sdk.html

Steve