On Mon, Sep 13, 2010, kyousuke_tsumura.fujifilm.co.jp wrote:
> First of all, I want you to clarify
> whether MD based on 3D-RISM can be used in AMBER11.
3D-RISM is available in AmberTools, which is available for free (using the
GPL license). As you have discovered, there is no interface to sander
in the current release. [For the curious: we have this implemented
internally, but our 3D-RISM code uses FFTW. We would need a special
license from MIT to distribute this linked to sander.]
Be sure to understand the limitations of the current implementations of
3D-RISM: although MD simulations are possible, they are rather slow, and there
are still important questions to be resolved about the physical realism of
integral equation results and about which closures to use. You should think
of AmberTools as providing a platform for research into integral equation
methods, and not as something to just routinely apply in MD simulations.
...dac
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Received on Mon Sep 13 2010 - 06:30:03 PDT
