[gmx-users] Polarisation model
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 7 11:35:58 CET 2012
On 2012-11-07 11:24, Volker Lesch wrote:
> On 11/07/2012 11:19 AM, David van der Spoel wrote:
>> On 2012-11-07 10:21, Volker Lesch wrote:
>>> Dear all,
>>> I am a new Gromacs user. In the past I used AMBER, but because of
>>> performance and technical reason I want to switch to Gromacs. Actually,
>>> I have one big problem namely polarisation. In AMBER I used the atomic
>>> point dipole model but this one is not implemented in Gromacs (please
>>> correct me if I am wrong). Are there any experienced data which compare
>>> the two models, atomic point dipole and shell??
>>> Kind regards,
>> This is not implemented. The shell model works but with limited
>> functionality, such that the Charmm model does not work completely. It
>> would be interesting to have such a comparison although I expect few
>> significant differences.
> thanks for this reply. So the shell model only works for simple systems
> like water. Is this correct? What are the exact limitations?
> Kind regards,
In Charmm there are additional terms for screening like the Thole
potential, which is implemented in gmx but not really debugged
thoroughly yet. However, the Charmm people also use some kind of
non-bonded screening that is not implemented.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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