[gmx-users] David, adding new atom types to gromacs "shell model"

[xieyh at hkusua.hku.hk]

Dear David:

On Tue, 2005-03-15 at 03:09 +0800, xieyh at hkusua.hku.hk wrote:
 
>> In detail, if a mass is given to shell, then we need not consider
>>[water_polarization] any more? Is it right? On the contrary, I just need to
>> define [bond], [angle] etc items for describing the connection of shell
>>particle to dummies or other atoms? Could you help me to confirm myself?
>>
>Yes you still have polarization but you do not optimize the shell
>position at each time step. This is the way e.g. DL_POLY treats shell
>particles.

I still have polarization? In shell model, the polarization is obtained from the
definition of [water_polarization] item in sw.itp.  However, where is the
polarization from in the case of giving a mass to shell particle? (can I delete
the [water_polarization] item in this case?)

I am not very sure. Is that realized by the changes of bond length between shell
particle and its connected atom (e.g. oxygen in water molecule)?

Thanks again.


Regards, 

Xie YH
Hong Kong Univ.