Fwd: RBCG tutorial

From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Wed Nov 11 2009 - 03:56:35 CST

I have examined the SBCG tutorial, which deals with a homodimer with
two identical subunits. If I understand, only one subunit was
simulated.

What about if the subunits of a multimer are not identical,
specifically not identical conformations? And what about if one wants
to deal with all subunits together because the shape depends also on
interaction among subunits?

Before coming across the SBCG tutorial, I have built SGCG and RBCG
models (with previous automatic generation of psf for the whole) of a
whole multimer, where the subunits differ slightly in length (problems
of X-ray diffr resolution) and markedly in shape. I wonder whether
this is a faulty approach, that is that only covalently-bound peptide
stretches can be cg-simulated with vmd-namd.

Thanks a lot for clarifying or comments, possibly for both SBCG and RBCG.

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
Date: Wed, Nov 11, 2009 at 10:08 AM
Subject: namd-l: RBCG tutorial
To: NAMD <namd-l_at_ks.uiuc.edu>

Is any residue-based tutorial available for coarse-grained MD? I am
aware of the SBCG tutorial.
thanks
francesco pietra

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