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

David spoel at xray.bmc.uu.se
Mon Mar 14 21:45:16 CET 2005

On Tue, 2005-03-15 at 04:19 +0800, xieyh at hkusua.hku.hk wrote:
> 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?)
No. If you delete the polarization the particle will be not connected.

> 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)?
Please check the itp file together with the manual (ch. 5), and the
accompanying paper.

> Thanks again.
> Regards, 
> Xie YH
> Hong Kong Univ.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list