Vitaly V. Chaban wrote:
On Thu, Oct 29, 2009 at 1:14 PM, David van der Spoel
<[email protected]> 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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--
========================================
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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