colvars and parallel-tempering with namd2.10

From: Francesco Pietra (
Date: Mon Aug 12 2013 - 09:54:25 CDT

My aim is to carry out parallel tempering of a transmembrane protein
endowed of peptide ligands in a periodic TIP3 box. I would like to
restrain all except the mobile parts of the protein. To this end I am
examining the multifaceted opportunities of colvars with MPI-compiled

I would be very grateful for an input on where, in the now quite
complex panorama of colvars, to concentrate attention in view of the
above task. My major concern is the large number of atoms to include
in colvars, which my well conflict with the "few thousand" set fort in
the manual. I.e., ca 20,000 protein + peptide atoms and, if I also
want to restrain the double-layer membrane, additional 27,000 atoms.

Thanks for advice

francesco pietra

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