[gmx-users] Polarizable models

[Justin A. Lemkul]

Vitaly V. Chaban wrote:
> On Thu, Oct 29, 2009 at 1:14 PM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> Vitaly V. Chaban wrote:
>>> Hi,
>>>
>>> Is there any place to read how gromacs treats polarizable models?
>>> The only thing I found in the official manual is that shells are
>>> denoted as "S" in the topology. What is especially interesting for me
>>> now is a concrete implementation and the ways of use.
>> Our old SW water model is in the distribution (sw.itp).
>> The reference to the paper is in there IIRC.
> 
> Could you please explain what's the difference between
> [water_polarization] and then [polarization] sections in sw.itp? What
> should be used instead of [water_polarization] in the case of another
> polarized molecule?
> 

These are controlled by an #ifdef block, for either anisotropic (-DANISOTROPIC) 
or isotropic (default) polarizability.  The reference at the top of sw.itp 
explains the difference between the two.

-Justin

> Thanks,
> Vitaly
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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